Methods and systems for analyzing targetable pathologic processes in covid-19 via gene expression analysis

ABSTRACT

The present disclosure provides systems and methods for machine learning classification and assessment of COVID-19 disease based on gene expression data. In an aspect, a method for determining a COVID-19 disease state of a subject may comprise: (a) assaying a biological sample obtained or derived from the subject to produce a data set comprising gene expression measurements of the biological sample at each of a plurality of COVID-19 disease-associated genomic loci; (b) computer processing the data set to determine the COVID-19 disease state of the subject; and (c) electronically outputting a report indicative of the COVID-19 disease state of the subject.

CROSS-REFERENCE

This application claims the benefit of U.S. Provisional Patent Application No. 63/023,088, filed May 11, 2020, which is incorporated by reference herein in its entirety.

BACKGROUND

SARS-CoV2 is a coronavirus and causative agent of the COVID-19 pandemic. COVID-19 typically causes mild respiratory symptoms, but may escalate to acute respiratory distress syndrome (ARDs) with an increased risk of respiratory failure and death. However, the trajectory of disease progression and the status of affected tissues in COVID-19 patients has not been elucidated. A comprehensive analysis of gene expression data from the blood, lung, and airway of COVID-19 patients is performed to investigate the host response to SARS-CoV2 infection. Results indicate that COVID-19 pathogenesis is driven by populations of myeloid-lineage cells with highly inflammatory but distinct transcriptional signatures, suggesting a progression in activation from the periphery to the lung tissue. In addition, through analysis of immune cells and inflammatory pathways enriched in each compartment, a model of the systemic response to SARS-CoV2 is constructed, and therapeutics targeting key upstream regulators of pathways contributing to COVID-19 pathogenesis are identified.

SUMMARY

In an aspect, the present disclosure provides a method of identifying one or more records having a specific phenotype, the method comprising: receiving a plurality of first records, wherein each first record is associated with one or more of a plurality of phenotypes; receiving a plurality of second records, wherein each second record is associated with one or more of the plurality of phenotypes, and wherein the plurality of second records and the plurality of first records are non-overlapping; applying a machine learning algorithm to at least one first record and at least one second record to determine a classifier; receiving a plurality of third records, wherein the third records are distinct from the plurality of first records and the plurality of second records; and applying the classifier to the plurality of third records to identify one or more third records associated with the specific phenotype.

In some embodiments, the first records and the second records comprise nucleic acid sequencing data, transcriptome data, genome data, epigenome data, proteome data, metabolome data, virome data, metabolome data, methylome data, lipidomic data, lineage-ome data, nucleosomal occupancy data, a genetic variant, a gene fusion, an insertion or deletion (indel), or any combination thereof. In some embodiments, the first records and the second records are in different formats. In some embodiments, the first records and the second records are from different sources, different studies, or both. In some embodiments, the phenotype comprises a disease state, an organ involvement, a medication response, or any combination thereof. In some embodiments, the classifier comprises an elastic generalized linear model classifier, a k-nearest neighbors classifier, a random forest classifier, or any combination thereof.

In some embodiments, the elastic generalized linear model classifier employs an elastic penalty of about 0.8 to about 1. In some embodiments, the elastic generalized linear model classifier employs an elastic penalty of at least about 0.8, about 0.825, about 0.85, about 0.875, about 0.9, about 0.925, about 0.95, about 0.975, or about 1. In some embodiments, the elastic generalized linear model classifier employs an elastic penalty of at most about 0.8, about 0.825, about 0.85, about 0.875, about 0.9, about 0.925, about 0.95, about 0.975, or about 1. In some embodiments, the elastic generalized linear model classifier employs an elastic penalty of about 0.8 to about 0.825, about 0.8 to about 0.85, about 0.8 to about 0.875, about 0.8 to about 0.9, about 0.8 to about 0.925, about 0.8 to about 0.95, about 0.8 to about 0.975, about 0.8 to about 1, about 0.825 to about 0.85, about 0.825 to about 0.875, about 0.825 to about 0.9, about 0.825 to about 0.925, about 0.825 to about 0.95, about 0.825 to about 0.975, about 0.825 to about 1, about 0.85 to about 0.875, about 0.85 to about 0.9, about 0.85 to about 0.925, about 0.85 to about 0.95, about 0.85 to about 0.975, about 0.85 to about 1, about 0.875 to about 0.9, about 0.875 to about 0.925, about 0.875 to about 0.95, about 0.875 to about 0.975, about 0.875 to about 1, about 0.9 to about 0.925, about 0.9 to about 0.95, about 0.9 to about 0.975, about 0.9 to about 1, about 0.925 to about 0.95, about 0.925 to about 0.975, about 0.925 to about 1, about 0.95 to about 0.975, about 0.95 to about 1, or about 0.975 to about 1. In some embodiments, the elastic generalized linear model classifier employs an elastic penalty of about 0.8, about 0.825, about 0.85, about 0.875, about 0.9, about 0.925, about 0.95, about 0.975, or about 1.

In some embodiments, the k-nearest neighbors classifier employs a K value of the size of the plurality of distinct first data sets, wherein k is about 1 to about 20. In some embodiments, the k-nearest neighbors classifier employs a K value of the size of the plurality of distinct first data sets, wherein k is at least about 1, about 2, about 3, about 4, about 5, about 6, about 8, about 10, about 12, about 14, about 16, or about 20. In some embodiments, the k-nearest neighbors classifier employs a K value of the size of the plurality of distinct first data sets, wherein k is at most about 1, about 2, about 3, about 4, about 5, about 6, about 8, about 10, about 12, about 14, about 16, or about 20. In some embodiments, the k-nearest neighbors classifier employs a K value of the size of the plurality of distinct first data sets, wherein k is about 1 to about 2, about 1 to about 3, about 1 to about 4, about 1 to about 5, about 1 to about 6, about 1 to about 8, about 1 to about 10, about 1 to about 12, about 1 to about 14, about 1 to about 16, about 1 to about 20, about 2 to about 3, about 2 to about 4, about 2 to about 5, about 2 to about 6, about 2 to about 8, about 2 to about 10, about 2 to about 12, about 2 to about 14, about 2 to about 16, about 2 to about 20, about 3 to about 4, about 3 to about 5, about 3 to about 6, about 3 to about 8, about 3 to about 10, about 3 to about 12, about 3 to about 14, about 3 to about 16, about 3 to about 20, about 4 to about 5, about 4 to about 6, about 4 to about 8, about 4 to about 10, about 4 to about 12, about 4 to about 14, about 4 to about 16, about 4 to about 20, about 5 to about 6, about 5 to about 8, about 5 to about 10, about 5 to about 12, about 5 to about 14, about 5 to about 16, about 5 to about 20, about 6 to about 8, about 6 to about 10, about 6 to about 12, about 6 to about 14, about 6 to about 16, about 6 to about 20, about 8 to about 10, about 8 to about 12, about 8 to about 14, about 8 to about 16, about 8 to about 20, about 10 to about 12, about 10 to about 14, about 10 to about 16, about 10 to about 20, about 12 to about 14, about 12 to about 16, about 12 to about 20, about 14 to about 16, about 14 to about 20, or about 16 to about 20. In some embodiments, the k-nearest neighbors classifier employs a K value of the size of the plurality of distinct first data sets, wherein k is about 1, about 2, about 3, about 4, about 5, about 6, about 8, about 10, about 12, about 14, about 16, or about 20.

In some embodiments, the K-value of the random forest classifier is incremented by 1 if the k-value is an even number. In some embodiments, applying a machine learning algorithm to the third data set comprises applying a machine learning algorithm to a plurality of unique third data sets.

In some embodiments, the classifier identifies said one or more third records associated with the specific phenotype with an accuracy of about 70% to about 100%. In some embodiments, the classifier identifies said one or more third records associated with the specific phenotype with an accuracy of at least about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100%. In some embodiments, the classifier identifies said one or more third records associated with the specific phenotype with an accuracy of at most about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100%. In some embodiments, the classifier identifies said one or more third records associated with the specific phenotype with an accuracy of about 70% to about 75%, about 70% to about 80%, about 70% to about 85%, about 70% to about 90%, about 70% to about 95%, about 70% to about 100%, about 75% to about 80%, about 75% to about 85%, about 75% to about 90%, about 75% to about 95%, about 75% to about 100%, about 80% to about 85%, about 80% to about 90%, about 80% to about 95%, about 80% to about 100%, about 85% to about 90%, about 85% to about 95%, about 85% to about 100%, about 90% to about 95%, about 90% to about 100%, or about 95% to about 100%. In some embodiments, the classifier identifies said one or more third records associated with the specific phenotype with an accuracy of about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100%.

In some embodiments, the classifier identifies said one or more third records associated with the specific phenotype with an accuracy of about 70% to about 100%. In some embodiments, the classifier identifies said one or more third records associated with the specific phenotype with an accuracy of at least about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100%. In some embodiments, the classifier identifies said one or more third records associated with the specific phenotype with an accuracy of at most about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100%. In some embodiments, the classifier identifies said one or more third records associated with the specific phenotype with an accuracy of about 70% to about 75%, about 70% to about 80%, about 70% to about 85%, about 70% to about 90%, about 70% to about 95%, about 70% to about 100%, about 75% to about 80%, about 75% to about 85%, about 75% to about 90%, about 75% to about 95%, about 75% to about 100%, about 80% to about 85%, about 80% to about 90%, about 80% to about 95%, about 80% to about 100%, about 85% to about 90%, about 85% to about 95%, about 85% to about 100%, about 90% to about 95%, about 90% to about 100%, or about 95% to about 100%. In some embodiments, the classifier identifies said one or more third records associated with the specific phenotype with an accuracy of about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100%.

In some embodiments, the classifier herein enables a specific phenotype association sensitivity of about 70% to about 100%. In some embodiments, the classifier herein enables a specific phenotype association sensitivity of at least 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100%. In some embodiments, the classifier herein enables a specific phenotype association sensitivity of at most 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100%. In some embodiments, the classifier herein enables a specific phenotype association sensitivity of about 70% to about 75%, about 70% to about 80%, about 70% to about 85%, about 70% to about 90%, about 70% to about 95%, about 70% to about 100%, about 75% to about 80%, about 75% to about 85%, about 75% to about 90%, about 75% to about 95%, about 75% to about 100%, about 80% to about 85%, about 80% to about 90%, about 80% to about 95%, about 80% to about 100%, about 85% to about 90%, about 85% to about 95%, about 85% to about 100%, about 90% to about 95%, about 90% to about 100%, or about 95% to about 100%. In some embodiments, the classifier herein enables a specific phenotype association sensitivity of about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100%.

In some embodiments, the classifier herein enables a specific phenotype association specificity of about 70% to about 100%. In some embodiments, the classifier herein enables a specific phenotype association specificity of at least 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100%. In some embodiments, the classifier herein enables a specific phenotype association specificity of at most 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100%. In some embodiments, the classifier herein enables a specific phenotype association specificity of about 70% to about 75%, about 70% to about 80%, about 70% to about 85%, about 70% to about 90%, about 70% to about 95%, about 70% to about 100%, about 75% to about 80%, about 75% to about 85%, about 75% to about 90%, about 75% to about 95%, about 75% to about 100%, about 80% to about 85%, about 80% to about 90%, about 80% to about 95%, about 80% to about 100%, about 85% to about 90%, about 85% to about 95%, about 85% to about 100%, about 90% to about 95%, about 90% to about 100%, or about 95% to about 100%. In some embodiments, the classifier herein enables a specific phenotype association specificity of about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100%.

In some embodiments, the method further comprises filtering the first records, the second records, or both. In some embodiments, the filtering comprises removing outliers, removing background noise, removing data without annotation data, normalizing, scaling, variance correcting, Weighted Gene Co-expression Network Analysis, enrichment analysis, dimensionality reduction, or any combination thereof. In some embodiments, the normalizing is performed by Robust Multi-Array Analysis (RMA), Guanine Cytosine Robust Multi-Array Analysis (GCRMA), Linear Models for Microarray Data, variance stabilizing transformation (VST), normal-exponential quantile correction (NEQC), or any combination thereof. In some embodiments, the variance correction comprises employing a local empirical Bayesian shrinkage, adjusting the p-values for multiple hypothesis testing using the Benjamini-Hochberg correction, and removing all data with a set false discovery rate

In some embodiments, the false discovery rate is about 0.000001 to about 0.2. In some embodiments, the false discovery rate is at least about 0.000001. In some embodiments, the false discovery rate is at most about 0.2. In some embodiments, the false discovery rate is about 0.000001 to about 0.00005, about 0.000001 to about 0.00001, about 0.000001 to about 0.0005, about 0.000001 to about 0.0001, about 0.000001 to about 0.005, about 0.000001 to about 0.001, about 0.000001 to about 0.05, about 0.000001 to about 0.01, about 0.000001 to about 0.2, about 0.00005 to about 0.00001, about 0.00005 to about 0.0005, about 0.00005 to about 0.0001, about 0.00005 to about 0.005, about 0.00005 to about 0.001, about 0.00005 to about 0.05, about 0.00005 to about 0.01, about 0.00005 to about 0.2, about 0.00001 to about 0.0005, about 0.00001 to about 0.0001, about 0.00001 to about 0.005, about 0.00001 to about 0.001, about 0.00001 to about 0.05, about 0.00001 to about 0.01, about 0.00001 to about 0.2, about 0.0005 to about 0.0001, about 0.0005 to about 0.005, about 0.0005 to about 0.001, about 0.0005 to about 0.05, about 0.0005 to about 0.01, about 0.0005 to about 0.2, about 0.0001 to about 0.005, about 0.0001 to about 0.001, about 0.0001 to about 0.05, about 0.0001 to about 0.01, about 0.0001 to about 0.2, about 0.005 to about 0.001, about 0.005 to about 0.05, about 0.005 to about 0.01, about 0.005 to about 0.2, about 0.001 to about 0.05, about 0.001 to about 0.01, about 0.001 to about 0.2, about 0.05 to about 0.01, about 0.05 to about 0.2, or about 0.01 to about 0.2. In some embodiments, the false discovery rate is about 0.000001, about 0.00005, about 0.00001, about 0.0005, about 0.0001, about 0.005, about 0.001, about 0.05, about 0.01, or about 0.2.

In some embodiments, the Weighted Gene Co-expression Network Analysis comprises calculating a topology matrix, clustering the data based on the topology matrix, and correlating module eigenvalues for traits on a linear scale by Pearson correlation, for nonparametric traits by Spearman correlation, and for dichotomous traits by point-biserial correlation or t-test. The Pearson correlation or the Product Moment Correlation Coefficient (PMCC), is a number between −1 and 1 that indicates the extent to which two variables are linearly related. The Spearman correlation is a nonparametric measure of rank correlation; statistical dependence between the rankings of two variables.

In some embodiments, the one or more records having a specific phenotype correspond to one or more subjects, and the method further comprises identifying the one or more subjects as (i) having a diagnosis of a disease state or condition, (ii) having a prognosis of a disease state or condition, (iii) being suitable or not suitable for enrollment in a clinical trial for a disease state or condition, (iv) being suitable or not suitable for being administered a therapeutic regimen configured to treat a disease state or condition, (v) having an efficacy or not having an efficacy of a therapeutic regimen configured to treat a disease state or condition, based at least in part on the specific phenotype corresponding to the one or more subjects.

In another aspect, the present disclosure provides a non-transitory computer-readable storage media encoded with a computer program including instructions executable by a processor to create an application for identifying one or more records having a specific phenotype, the application comprising: a first receiving module receiving a plurality of first records, wherein each first record is associated with one or more of a plurality of phenotypes; a second receiving module receiving a plurality of second records, wherein each second record is associated with one or more of the plurality of phenotypes, and wherein the plurality of second records and the plurality of first records are non-overlapping; a machine learning module applying a machine learning algorithm to at least one first record and at least one second record to determine a classifier; a third receiving module receiving a plurality of third records, wherein the third records are distinct from the plurality of first records and the plurality of second records; and a classifying module applying the classifier to the plurality of third records to identify one or more third records associated with the specific phenotype.

In some embodiments, the first records and the second records comprise nucleic acid sequencing data, transcriptome data, genome data, epigenome data, proteome data, metabolome data, virome data, metabolome data, methylome data, lipidomic data, lineage-ome data, nucleosomal occupancy data, a genetic variant, a gene fusion, an insertion or deletion (indel), or any combination thereof. In some embodiments, the first records and the second records are in different formats. In some embodiments, the first records and the second records are from different sources, different studies, or both. In some embodiments, the phenotype comprises a disease state, an organ involvement, a medication response, or any combination thereof. In some embodiments, the classifier comprises an elastic generalized linear model classifier, a k-nearest neighbors classifier, a random forest classifier, or any combination thereof. In some embodiments, the elastic generalized linear model classifier employs an elastic penalty of about 0.9. In some embodiments, the k-nearest neighbors classifier employs a K-value of about 5% of the size of the plurality of distinct first data sets. In some embodiments, the K-value of the random forest classifier is incremented by 1 if the k-value is an even number. In some embodiments, applying a machine learning algorithm to the third data set comprises applying a machine learning algorithm to a plurality of unique third data sets. In some embodiments, said classifier identifies said one or more third records associated with the specific phenotype with an accuracy of at least about 70%. In some embodiments, the method further comprises filtering the first records, the second records, or both. In some embodiments, the filtering comprises removing outliers, removing background noise, removing data without annotation data, normalizing, scaling, variance correcting, Weighted Gene Co-expression Network Analysis, enrichment analysis, dimensionality reduction, or any combination thereof. In some embodiments, the normalizing is performed by Robust Multi-Array Analysis (RMA), Guanine Cytosine Robust Multi-Array Analysis (GCRMA), Linear Models for Microarray Data, variance stabilizing transformation (VST), normal-exponential quantile correction (NEQC), or any combination thereof. In some embodiments, the variance correction comprises employing a local empirical Bayesian shrinkage, adjusting the p-values for multiple hypothesis testing using the Benjamini-Hochberg correction, and removing all data with a false discovery rate of less than 0.2. In some embodiments, the Weighted Gene Co-expression Network Analysis comprises calculating a topology matrix, clustering the data based on the topology matrix, and correlating module eigenvalues for traits on a linear scale by Pearson correlation, for nonparametric traits by Spearman correlation, and for dichotomous traits by point-biserial correlation or t-test.

In another aspect, the present disclosure provides a method for identifying a disease state or a susceptibility thereof of a subject, comprising: (a) using an assay to process a biological sample derived from the subject to generate a quantitative measure of each of a plurality of disease-associated genomic loci; (b) processing the dataset to identify the disease state or the susceptibility thereof of the subject; and (c) electronically outputting a report indicative of the disease state or the susceptibility thereof of the subject.

In some embodiments, the plurality of quantitative measures comprises gene expression measurements. In some embodiments, the disease state comprises an active COVID-19 condition or an inactive COVID-19 condition.

In another aspect, the present disclosure provides a computer-implemented method for assessing a disease state or condition of a subject, comprising: (a) receiving a dataset of a biological sample of the subject; (b) selecting one or more data analysis tools, wherein the one or more data analysis tools comprise an analysis tool selected from the group consisting of: a BIG-C™ big data analysis tool, an I-Scope™ big data analysis tool, a T-Scope™ big data analysis tool, a CellScan big data analysis tool, an MS (Molecular Signature) Scoring™ analysis tool, a Gene Set Variation Analysis (GSVA) tool (e.g., P-Scope), and a combination thereof; (c) processing the dataset using the one or more data analysis tools to generate a data signature of the biological sample of the subject; and (d) based at least in part on the data signature generated in (c), assessing the disease state or condition of the subject.

In some embodiments, the dataset comprises gene expression measurements. In some embodiments, the disease state comprises an active COVID-19 condition or an inactive COVID-19 condition.

In some embodiments, the dataset comprises mRNA gene expression or transcriptome data, DNA genomic data, proteomic data, metabolomic data, or a combination thereof. In some embodiments, the biological sample is selected from the group consisting of: a whole blood (WB) sample, a PBMC sample, a tissue sample, and a cell sample. In some embodiments, assessing the condition of the subject comprises identifying a disease or disorder of the subject.

In some embodiments, the method further comprises identifying a disease or disorder of the subject at a sensitivity or specificity of at least about 70%. In some embodiments, the method further comprises determining a likelihood of the identification of the disease or disorder of the subject. In some embodiments, the method further comprises providing a therapeutic intervention for the disease or disorder of the subject. In some embodiments, the method further comprises monitoring the disease or disorder of the subject, wherein the monitoring comprises assessing the disease or disorder of the subject at a plurality of time points, wherein the assessing is based at least on the disease or disorder identified at each of the plurality of time points.

In some embodiments, selecting the one or more data analysis tools comprises receiving a user selection of the one or more data analysis tools. In some embodiments, selecting the one or more data analysis tools is automatically performed by the computer without receiving a user selection of the one or more data analysis tools.

In another aspect, the present disclosure provides a computer system for assessing a disease state or condition of a subject, comprising: a database that is configured to store a dataset of a biological sample of the subject; and one or more computer processors operatively coupled to the database, wherein the one or more computer processors are individually or collectively programmed to: (i) select one or more data analysis tools, wherein the one or more data analysis tools comprise an analysis tool selected from the group consisting of: a BIG-C™ big data analysis tool, an I-Scope™ big data analysis tool, a T-Scope™ big data analysis tool, a CellScan big data analysis tool, an MS (Molecular Signature) Scoring™ analysis tool, a Gene Set Variation Analysis (GSVA) tool (e.g., P-Scope), and a combination thereof; (ii) process the dataset using the one or more data analysis tools to generate a data signature of the biological sample of the subject; and (iii) based at least in part on the data signature generated in (ii), assess the disease state or condition of the subject.

In some embodiments, the dataset comprises gene expression measurements. In some embodiments, the disease state comprises an active COVID-19 condition or an inactive COVID-19 condition.

In another aspect, the present disclosure provides a non-transitory computer-readable medium comprising machine-executable code that, upon execution by one or more computer processors, implements a method for assessing a disease state or condition of a subject, the method comprising: (a) receiving a dataset of a biological sample of the subject; (b) selecting one or more data analysis tools, wherein the one or more data analysis tools comprise an analysis tool selected from the group consisting of: a BIG-C™ big data analysis tool, an I-Scope™ big data analysis tool, a T-Scope™ big data analysis tool, a CellScan big data analysis tool, an MS (Molecular Signature) Scoring™ analysis tool, a Gene Set Variation Analysis (GSVA) tool (e.g., P-Scope), and a combination thereof (c) processing the dataset using the one or more data analysis tools to generate a data signature of the biological sample of the subject; and (d) based at least in part on the data signature generated in (c), assessing the disease state or condition of the subject.

In some embodiments, the dataset comprises gene expression measurements. In some embodiments, the disease state comprises an active COVID-19 condition or an inactive COVID-19 condition.

In any embodiment described herein, the one or more data analysis tools can be a plurality of data analysis tools each independently selected from a BIG-C™ big data analysis tool, an I-Scope™ big data analysis tool, a T-Scope™ big data analysis tool, a CellScan big data analysis tool, an MS (Molecular Signature) Scoring™ analysis tool, a Gene Set Variation Analysis (GSVA) tool (e.g., P-Scope), and a combination thereof.

In another aspect, the present disclosure provides a method for determining a COVID-19 disease state of a subject, comprising: (a) assaying a biological sample obtained or derived from the subject to produce a data set comprising gene expression measurements of the biological sample at each of a plurality of COVID-19 disease-associated genomic loci, wherein the plurality of COVID-19 disease-associated genomic loci comprises at least a portion of a gene selected from the group of genes listed in Table 6 and Tables 7A-7C; (b) computer processing the data set to determine the COVID-19 disease state of the subject; and (c) electronically outputting a report indicative of the COVID-19 disease state of the subject.

In some embodiments, the plurality of COVID-19 disease-associated genomic loci comprises at least a portion of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000, 5100, 5200, 5300, 5400, 5500, 5600, 5700, 5800, 5900, or 6000 genes selected from the group of genes listed in Table 6 and Tables 7A-7C.

In some embodiments, the method further comprises determining the COVID-19 disease state of the subject with an accuracy of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the method further comprises determining the COVID-19 disease state of the subject with a sensitivity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the method further comprises determining the COVID-19 disease state of the subject with a specificity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the method further comprises determining the COVID-19 disease state of the subject with a positive predictive value of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the method further comprises determining the COVID-19 disease state of the subject with a negative predictive value of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the method further comprises determining the COVID-19 disease state of the subject with an Area-Under-Curve (AUC) of at least about 0.50, at least about 0.55, at least about 0.60, at least about 0.65, at least about 0.70, at least about 0.75, at least about 0.80, at least about 0.85, at least about 0.90, at least about 0.91, at least about 0.92, at least about 0.93, at least about 0.94, at least about 0.95, at least about 0.96, at least about 0.97, at least about 0.98, at least about 0.99, or more than about 0.99.

In some embodiments, the subject has received a diagnosis of the COVID-19 disease. In some embodiments, the subject is suspected of having the COVID-19 disease. In some embodiments, the subject is at elevated risk of having the COVID-19 disease or having severe complications from the COVID-19 disease. In some embodiments, the subject is asymptomatic for the COVID-19 disease. In some embodiments, the method further comprises administering a treatment to the subject based at least in part on the determined COVID-19 disease state. In some embodiments, the treatment is configured to treat the COVID-19 disease state of the subject. In some embodiments, the treatment is configured to reduce a severity of the COVID-19 disease state of the subject. In some embodiments, the treatment is configured to reduce a risk of having the COVID-19 disease. In some embodiments, the treatment comprises a drug. In some embodiments, the drug is selected from the group listed in Tables 8A-8B.

In some embodiments, (b) comprises using a trained machine learning classifier to analyze the data set to determine the COVID-19 disease state of the subject. In some embodiments, the trained machine learning classifier is trained using gene expression data obtained by a data analysis tool selected from the group consisting of: a BIG-C™ big data analysis tool, an I-Scope™ big data analysis tool, a T-Scope™ big data analysis tool, a CellScan big data analysis tool, an MS (Molecular Signature) Scoring™ analysis tool, and a Gene Set Variation Analysis (GSVA) tool. In some embodiments, the trained machine learning classifier is selected from the group consisting of a linear regression, a logistic regression, a Ridge regression, a Lasso regression, an elastic net (EN) regression, a support vector machine (SVM), a gradient boosted machine (GBM), a k nearest neighbors (kNN), a generalized linear model (GLM), a naïve Bayes (NB) classifier, a neural network, a Random Forest (RF), a deep learning algorithm, and a combination thereof.

In some embodiments, (b) comprises comparing the data set to a reference data set. In some embodiments, the reference data set comprises gene expression measurements of reference biological samples at each of the plurality of COVID-19 disease-associated genomic loci. In some embodiments, the reference biological samples comprise a first plurality of biological samples obtained or derived from subjects having the COVID-19 disease and a second plurality of biological samples obtained or derived from subjects not having the COVID-19 disease.

In some embodiments, the biological sample is selected from the group consisting of: a blood sample, isolated peripheral blood mononuclear cells (PBMCs), a biopsy sample, and any derivative thereof.

In some embodiments, the method further comprises determining a likelihood of the determined COVID-19 disease state.

In some embodiments, the method further comprises monitoring the COVID-19 disease state of the subject, wherein the monitoring comprises assessing the COVID-19 disease state of the subject at a plurality of time points.

In some embodiments, a difference in the assessment of the COVID-19 disease state of the subject among the plurality of time points is indicative of one or more clinical indications selected from the group consisting of: (i) a diagnosis of the COVID-19 disease state of the subject, (ii) a prognosis of the COVID-19 disease state of the subject, and (iii) an efficacy or non-efficacy of a course of treatment for treating the COVID-19 disease state of the subject.

In another aspect, the present disclosure provides a computer system for determining a COVID-19 disease state of a subject, comprising: a database that is configured to store a dataset comprising gene expression data, wherein the gene expression data is obtained by assaying a biological sample obtained or derived from the subject to produce gene expression measurements of the biological sample at each of a plurality of COVID-19 disease-associated genomic loci, wherein the plurality of COVID-19 disease-associated genomic loci comprises at least a portion of a gene selected from the group of genes listed in Table 6 and Tables 7A-7C; and one or more computer processors operatively coupled to the database, wherein the one or more computer processors are individually or collectively programmed to: (i) computer process the data set to determine the COVID-19 disease state of the subject; (ii) electronically output a report indicative of the COVID-19 disease state of the subject.

In some embodiments, the plurality of COVID-19 disease-associated genomic loci comprises at least a portion of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000, 5100, 5200, 5300, 5400, 5500, 5600, 5700, 5800, 5900, or 6000 genes selected from the group of genes listed in Table 6 and Tables 7A-7C.

In some embodiments, the one or more computer processors are individually or collectively programmed to further determine the COVID-19 disease state of the subject with an accuracy of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the one or more computer processors are individually or collectively programmed to further determine the COVID-19 disease state of the subject with a sensitivity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the one or more computer processors are individually or collectively programmed to further determine the COVID-19 disease state of the subject with a specificity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the one or more computer processors are individually or collectively programmed to further determine the COVID-19 disease state of the subject with a positive predictive value of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the one or more computer processors are individually or collectively programmed to further determine the COVID-19 disease state of the subject with a negative predictive value of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the one or more computer processors are individually or collectively programmed to further determine the COVID-19 disease state of the subject with an Area-Under-Curve (AUC) of at least about 0.50, at least about 0.55, at least about 0.60, at least about 0.65, at least about 0.70, at least about 0.75, at least about 0.80, at least about 0.85, at least about 0.90, at least about 0.91, at least about 0.92, at least about 0.93, at least about 0.94, at least about 0.95, at least about 0.96, at least about 0.97, at least about 0.98, at least about 0.99, or more than about 0.99.

In some embodiments, the subject has received a diagnosis of the COVID-19 disease. In some embodiments, the subject is suspected of having the COVID-19 disease. In some embodiments, the subject is at elevated risk of having the COVID-19 disease or having severe complications from the COVID-19 disease. In some embodiments, the subject is asymptomatic for the COVID-19 disease. In some embodiments, the one or more computer processors are individually or collectively programmed to further direct a treatment to be administered to the subject based at least in part on the determined COVID-19 disease state. In some embodiments, the treatment is configured to treat the COVID-19 disease state of the subject. In some embodiments, the treatment is configured to reduce a severity of the COVID-19 disease state of the subject. In some embodiments, the treatment is configured to reduce a risk of having the COVID-19 disease. In some embodiments, the treatment comprises a drug. In some embodiments, the drug is selected from the group listed in Tables 8A-8B.

In some embodiments, (i) comprises using a trained machine learning classifier to analyze the data set to determine the COVID-19 disease state of the subject. In some embodiments, the trained machine learning classifier is trained using gene expression data obtained by a data analysis tool selected from the group consisting of: a BIG-C™ big data analysis tool, an I-Scope™ big data analysis tool, a T-Scope™ big data analysis tool, a CellScan big data analysis tool, an MS (Molecular Signature) Scoring™ analysis tool, and a Gene Set Variation Analysis (GSVA) tool. In some embodiments, the trained machine learning classifier is selected from the group consisting of a linear regression, a logistic regression, a Ridge regression, a Lasso regression, an elastic net (EN) regression, a support vector machine (SVM), a gradient boosted machine (GBM), a k nearest neighbors (kNN), a generalized linear model (GLM), a naïve Bayes (NB) classifier, a neural network, a Random Forest (RF), a deep learning algorithm, and a combination thereof.

In some embodiments, (i) comprises comparing the data set to a reference data set. In some embodiments, the reference data set comprises gene expression measurements of reference biological samples at each of the plurality of COVID-19 disease-associated genomic loci. In some embodiments, the reference biological samples comprise a first plurality of biological samples obtained or derived from subjects having the COVID-19 disease and a second plurality of biological samples obtained or derived from subjects not having the COVID-19 disease.

In some embodiments, the biological sample is selected from the group consisting of: a blood sample, isolated peripheral blood mononuclear cells (PBMCs), a biopsy sample, and any derivative thereof.

In some embodiments, the one or more computer processors are individually or collectively programmed to further determine a likelihood of the determined COVID-19 disease state.

In some embodiments, the one or more computer processors are individually or collectively programmed to further monitor the COVID-19 disease state of the subject, wherein the monitoring comprises assessing the COVID-19 disease state of the subject at a plurality of time points.

In some embodiments, a difference in the assessment of the COVID-19 disease state of the subject among the plurality of time points is indicative of one or more clinical indications selected from the group consisting of: (i) a diagnosis of the COVID-19 disease state of the subject, (ii) a prognosis of the COVID-19 disease state of the subject, and (iii) an efficacy or non-efficacy of a course of treatment for treating the COVID-19 disease state of the subject.

In another aspect, the present disclosure provides a non-transitory computer readable medium comprising machine-executable code that, upon execution by one or more computer processors, implements a method for determining a COVID-19 disease state of a subject, the method comprising: (a) assaying a biological sample obtained or derived from the subject to produce a data set comprising gene expression measurements of the biological sample at each of a plurality of COVID-19 disease-associated genomic loci, wherein the plurality of COVID-19 disease-associated genomic loci comprises at least a portion of a gene selected from the group of genes listed in Table 6 and Tables 7A-7C; (b) computer processing the data set to determine the COVID-19 disease state of the subject; and (c) electronically outputting a report indicative of the COVID-19 disease state of the subject.

In some embodiments, the plurality of COVID-19 disease-associated genomic loci comprises at least a portion of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000, 5100, 5200, 5300, 5400, 5500, 5600, 5700, 5800, 5900, or 6000 genes selected from the group of genes listed in Table 6 and Tables 7A-7C.

In some embodiments, the method further comprises determining the COVID-19 disease state of the subject with an accuracy of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the method further comprises determining the COVID-19 disease state of the subject with a sensitivity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the method further comprises determining the COVID-19 disease state of the subject with a specificity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the method further comprises determining the COVID-19 disease state of the subject with a positive predictive value of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the method further comprises determining the COVID-19 disease state of the subject with a negative predictive value of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.

In some embodiments, the method further comprises determining the COVID-19 disease state of the subject with an Area-Under-Curve (AUC) of at least about 0.50, at least about 0.55, at least about 0.60, at least about 0.65, at least about 0.70, at least about 0.75, at least about 0.80, at least about 0.85, at least about 0.90, at least about 0.91, at least about 0.92, at least about 0.93, at least about 0.94, at least about 0.95, at least about 0.96, at least about 0.97, at least about 0.98, at least about 0.99, or more than about 0.99.

In some embodiments, the subject has received a diagnosis of the COVID-19 disease. In some embodiments, the subject is suspected of having the COVID-19 disease. In some embodiments, the subject is at elevated risk of having the COVID-19 disease or having severe complications from the COVID-19 disease. In some embodiments, the subject is asymptomatic for the COVID-19 disease. In some embodiments, the method further comprises administering a treatment to the subject based at least in part on the determined COVID-19 disease state. In some embodiments, the treatment is configured to treat the COVID-19 disease state of the subject. In some embodiments, the treatment is configured to reduce a severity of the COVID-19 disease state of the subject. In some embodiments, the treatment is configured to reduce a risk of having the COVID-19 disease. In some embodiments, the treatment comprises a drug. In some embodiments, the drug is selected from the group listed in Tables 8A-8B.

In some embodiments, (b) comprises using a trained machine learning classifier to analyze the data set to determine the COVID-19 disease state of the subject. In some embodiments, the trained machine learning classifier is trained using gene expression data obtained by a data analysis tool selected from the group consisting of: a BIG-C™ big data analysis tool, an I-Scope™ big data analysis tool, a T-Scope™ big data analysis tool, a CellScan big data analysis tool, an MS (Molecular Signature) Scoring™ analysis tool, and a Gene Set Variation Analysis (GSVA) tool. In some embodiments, the trained machine learning classifier is selected from the group consisting of a linear regression, a logistic regression, a Ridge regression, a Lasso regression, an elastic net (EN) regression, a support vector machine (SVM), a gradient boosted machine (GBM), a k nearest neighbors (kNN), a generalized linear model (GLM), a naïve Bayes (NB) classifier, a neural network, a Random Forest (RF), a deep learning algorithm, and a combination thereof.

In some embodiments, (b) comprises comparing the data set to a reference data set. In some embodiments, the reference data set comprises gene expression measurements of reference biological samples at each of the plurality of COVID-19 disease-associated genomic loci. In some embodiments, the reference biological samples comprise a first plurality of biological samples obtained or derived from subjects having the COVID-19 disease and a second plurality of biological samples obtained or derived from subjects not having the COVID-19 disease.

In some embodiments, the biological sample is selected from the group consisting of: a blood sample, isolated peripheral blood mononuclear cells (PBMCs), a biopsy sample, and any derivative thereof.

In some embodiments, the method further comprises determining a likelihood of the determined COVID-19 disease state.

In some embodiments, the method further comprises monitoring the COVID-19 disease state of the subject, wherein the monitoring comprises assessing the COVID-19 disease state of the subject at a plurality of time points.

In some embodiments, a difference in the assessment of the COVID-19 disease state of the subject among the plurality of time points is indicative of one or more clinical indications selected from the group consisting of: (i) a diagnosis of the COVID-19 disease state of the subject, (ii) a prognosis of the COVID-19 disease state of the subject, and (iii) an efficacy or non-efficacy of a course of treatment for treating the COVID-19 disease state of the subject.

Another aspect of the present disclosure provides a non-transitory computer-readable medium comprising machine executable code that, upon execution by one or more computer processors, implements any of the methods above or elsewhere herein.

Another aspect of the present disclosure provides a system comprising one or more computer processors and computer memory coupled thereto. The computer memory comprises machine executable code that, upon execution by the one or more computer processors, implements any of the methods above or elsewhere herein.

Additional aspects and advantages of the present disclosure will become readily apparent to those skilled in this art from the following detailed description, wherein only illustrative embodiments of the present disclosure are shown and described. As will be realized, the present disclosure is capable of other and different embodiments, and its several details are capable of modifications in various obvious respects, all without departing from the disclosure. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent application file contains at least one drawing executed in color. Copies of this patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings of which:

FIG. 1A shows transcriptional changes in the progression of the pathologic response to SARS-CoV2 traced through three compartments (blood, lung, and airway) from activation and mobilization of immune cells in the blood, to infiltration into the lung tissue and airway of infected patients.

FIGS. 1B-1D show differences in inflammatory pathways and immune cell types enriched in COVID-19 patients as compared to healthy controls as well those that were differentially enriched between the blood, lung, and airway compartments, including increased inflammatory pathway signatures (FIG. 1B), decreased lymphoid cell signatures (FIG. 1C), and increased myeloid cell signatures (FIG. 1D) in COVID-19 patients.

FIGS. 2A-2F show differential expression of specific genes of interest (FIGS. 2A-2B); GSVA enrichment of non-hematopoietic cell type gene signatures including fibroblasts, Type I and Type II alveolar cells, ciliated lung cells, club cells, and a general lung tissue cell signature (FIGS. 2C-2E); and increased expression of the viral entry genes ACE2 and TMPRSS2, which are typically expressed on lung epithelium (ref), in the airway of SARS-CoV2-infected patients (FIG. 2F).

FIGS. 3A-3F show that PBMC cluster 8 was dominated by an inflammatory monocyte population defined by C2, C5, CXCL10, CCR2 and multiple interferon-stimulated genes, whereas cluster 3 contained hallmarks of alternatively activated (M2) macrophages and/or myeloid-derived suppressor cells (MDSCs), including CD33, CD36, CD93 and ITGAM (FIG. 3A; similar to the blood, lung-derived monocyte/myeloid genes segregated into clusters associated with common myeloid-lineage cell functions, such as chemotaxis and pattern recognition, as well as multiple subpopulations (FIG. 3E);

FIGS. 4A-4D show GSVA evaluation of both monocyte cell surface and monocyte secreted gene expression confirmed heterogeneous cell surface markers in the BAL, and increased chemokine secretion in the lung (FIG. 4A); Each cluster was evaluated in its respective tissue sample and control by GSVA (FIG. 4B); comparison of the co-expressed genes between each tissue myeloid population shows that many of the increased genes in each tissue are shared (FIG. 4C); and significant overlap, as determined by Fisher's Exact Test, in many populations (FIG. 4D).

FIGS. 5A-5E show myeloid cell population in the PBMCs was found to be highly glycolytic, whereas there was no significant change to metabolism detected in the lung, and the population in the BAL was reliant on OXPHOS (FIG. 5A); although myeloid cell signatures were associated with the NLRP3 inflammasome in the PBMCs and lungs, this association was not found in the BAL (FIG. 5B); the classical complement cascade was significantly correlated with the increased myeloid cells in both PBMCs and BAL, whereas the alternative complement cascade was significantly correlated with the myeloid cells in the lung (FIG. 5C); the myeloid cells in the PBMCs were also significantly correlated with the cell cycle, but this may be more evident of plasma cells in the blood (FIG. 5D); additionally, the lung and BAL myeloid populations were negatively correlated with apoptosis (FIG. 5E).

FIGS. 6A-6B show results from pathway analysis on DEGs from each of the peripheral blood, lung, and airway compartments using IPA canonical signaling pathway and upstream regulator analysis functions, including that interferon signaling, the inflammasome, and other components of antiviral, innate immunity were reflected by the disease state gene expression profile compared to healthy controls (FIG. 6A); and that upstream regulators predicted to mediate responses to the virus in each compartment indicated uniform involvement of proinflammatory cytokines with type I interferon regulation dominant in the diseased lung (FIG. 6B).

FIG. 7 shows that by comparing DE results from multiple compartments (the blood, lung, and airway) in COVID-19 patients, we have developed a model of the systemic pathogenic response to SARS-CoV2 infection.

FIGS. 8A-8C show previously defined gene modules characterizing immune and inflammatory cells and processes.

FIGS. 9A-9B show increased expression of Type I interferon genes (IFNA4, IFNA6, IFNA10) and significant enrichment of the Type I and Type II IGS specifically in the lung tissue, but not in the blood or airway of COVID-19 patients.

FIGS. 10A-10C show GSVA enrichment of non-hematopoietic cell type gene signatures including fibroblasts, Type I and Type II alveolar cells, ciliated lung cells, club cells, and a general lung tissue cell signature.

FIGS. 11A-11D show that peripheral blood exhibited profoundly suppressed T cells determined by the downregulation of T cell activation markers CD28, LCK and ITK (FIG. 11A); metabolic function in the lung was varied, however, upregulated genes segregated with glycolysis, potentially reflecting cellular activation (cluster 18), whereas OXPHOS was predominantly downregulated along with other nuclear processes (transcription and mRNA processing) (FIG. 11B); similar to the PBMC compartment, T cells were decreased in the airway (FIGS. 11A and 11C); non-hematopoietic cell signatures in the BAL were similar in content to those derived from in vitro COVID19-infected lung epithelium primary cell lines (NHBE) REF (FIG. 11D);

FIGS. 12A-12F show upregulation of FCN1 (cluster 15), SELL (cluster 14) and S100A8/A9 (cluster 4) which comprise an inflammatory monocyte signature (G1 population) derived from the BAL fluid of COVID patients recently described by Liao et al. (FIG. 12A); the G1 and G2 population genes, characterized by predominately interferon-stimulated genes, were increased in the lung (FIG. 12B); conversely, the “novel intermediate macrophage” population (G2) characterized by inflammatory mediators and chemokines such as CCL2, CCL3 and CCL4, was increased in the BAL, but not the PBMCs (FIG. 12C); additionally, per patient analyses confirmed the presence of the “pro-fibrotic, SPP1+” macrophage (G3) and “lung alveolar macrophage” populations (G4) in the BAL, although there also may be some evidence of these populations in the lung (FIGS. 12D-12E); evidence of recently described alveolar macrophages (AMs; G4 population) specifically in the airway (Liao et al., 2020), although these markers were distributed among multiple clusters, including FABP4 and PPARG in cluster 17, SPP1 and MRC1 in cluster 10, and MARCO and TFRC in clusters 34 and 7, respectively (FIG. 12E); and comparison of this population with additional previously defined myeloid populations demonstrated significant overlap with IFN-activated macrophages, CX3CR1+ lining macrophages (arthritis model) and an alveolar macrophage phenotype (FIG. 12F).

FIGS. 13A-13C show that DE interrogation of all possible myeloid cell-specific genes demonstrated further heterogeneity in expression of markers, such as CD14, CD300C, and OSCAR between compartments.

FIG. 14 shows that for each gene, a Pearson correlation coefficient was calculated with every other myeloid cell gene for both the samples and controls in each tissue compartment; and the resultant correlation coefficient matrices were then hierarchically clustered into two clusters based upon co-expression.

FIGS. 15A-15E show results from evaluating metabolism in each compartment using GSVA, including that the TCA cycle was significantly increased in PBMCs, whereas OXPHOS is significantly increased in the BAL (FIGS. 15C-15D), and that additionally, pro-cell cycle genes were increased in PBMCs and pro-apoptosis genes were decreased.

FIG. 16 shows a computer system 1601 that is programmed or otherwise configured to, for example, perform methods of the disclosure.

FIG. 17 shows conserved and differential enrichment of immune cells and pathways in blood, lung, and airway of SARS-CoV2-infected patients.

FIGS. 18A-18C show elevated IFN expression in the lung tissue of COVID-19 patients. FIG. 18A: Normalized log 2 fold change RNA-seq expression values for IFN-associated genes from blood, lung, and airway of individual COVID-19 patients. The dotted line represents the expression of each gene in healthy individuals (for blood and lung) or PBMCs from COVID-19 patients (airway). FIG. 18B: Individual sample gene expression from the blood, lung, and airway was analyzed by GSVA for enrichment of IFN-related gene signatures. FIG. 18C: Normalized log 2 fold change RNA-seq expression values for anti-viral genes as in (section a). Generated using GraphPad Prism v8.4.2 (www.graphpad.com). #p<0.2, ##p<0.1, *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001

FIGS. 19A-19D show that viral entry gene expression correlates with enhanced expression of inflammatory mediators in SARS-CoV2-infected lungs. FIGS. 19A-19B: Normalized log 2 fold change RNA-seq expression values for chemokines and chemokine receptors (section a) and IL-1 family members (FIG. 19B) from blood, lung, and airway of COVID-19 patients as in FIG. 18A. FIG. 19C: Individual sample gene expression from the blood, lung, and airway was analyzed by GSVA for enrichment of various lung tissue cell categories. FIG. 19D: Normalized log 2 fold change RNA-seq expression values for viral entry genes as in FIGS. 19A-19B. Generated using GraphPad Prism v8.4.2 (www.graphpad.com). #p<0.2, ##p<0.1, *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001

FIGS. 20A-20F show that PPI analysis identifies different myeloid cell subsets and metabolic pathways in blood, lung, and airway of COVID-19 patients.

FIGS. 21A-21F show that different co-expression-derived myeloid populations are found in blood, lung, and airway of COVID-19 patients.

FIG. 22 shows an analysis of biological activities of myeloid subpopulations.

FIGS. 23A-23B show a pathway analysis of SARS-CoV-2 blood, lung, and airway.

FIG. 24 shows a graphical model of COVID-19 pathogenesis.

FIGS. 25A-25D show that metaclusters identify differentially expressed cell populations and functional gene clusters in SARS-CoV2 infected tissues and cell lines.

FIGS. 26A-26F shows an evaluation of macrophage gene signatures in myeloid-derived clusters from COVID-affected blood, lung and BAL fluid.

FIG. 27 shows heterogeneous expression of monocyte/myeloid cell genes in different CoV2 tissue compartments as compared to control.

FIG. 28 shows an analysis of biological activities of myeloid subpopulations.

FIGS. 29A-29E show a pathway analysis of SARS-CoV-2 lung tissue. FIG. 29A: Remaining significant upstream regulators operative in SARS-CoV-2 lung tissue predicted by IPA upstream regulator analysis. Upstream regulator analysis was also conducted on DEGs from each individual COVID-19 lung compared to healthy controls due to observed heterogeneity. FIG. 29B: significant results displayed for Lung1-CoV2 vs. Lung-CTL. FIG. 29C: significant results displayed for Lung2-CoV2 vs. Lung-CTL. Chemical reagents, chemical toxicants, and non-mammalian endogenous chemicals were culled from results. The boxes with the dotted outline separate small molecules/drugs/compounds that were predicted as upstream regulators from pathway molecules and complexes. FIGS. 29D-29E: IPA canonical signaling pathway analysis was conducted on individual COVID-19 lung samples. Pathways and upstream regulators were considered significant by |Activation Z-Score|≥2 and overlap p-value <0.01.

DETAILED DESCRIPTION

Unless otherwise defined, all technical terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs.

Certain Terms

As used herein, the singular forms “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. Any reference to “or” herein is intended to encompass “and/or” unless otherwise stated.

As used herein, the term “about” refers to an amount that is near the stated amount by 10%, 5%, or 1%, including increments therein.

As used herein, the phrases “at least one”, “one or more”, and “and/or” are open-ended expressions that are both conjunctive and disjunctive in operation. For example, each of the expressions “at least one of A, B and C”, “at least one of A, B, or C”, “one or more of A, B, and C”, “one or more of A, B, or C” and “A, B, and/or C” means A alone, B alone, C alone, A and B together, A and C together, B and C together, or A, B and C together.

As used herein, the singular forms “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. Any reference to “or” herein is intended to encompass “and/or” unless otherwise stated.

As used herein, the term “subject” refers to an entity or a medium that has testable or detectable genetic information. A subject can be a person, individual, or patient. A subject can be a vertebrate, such as, for example, a mammal. Non-limiting examples of mammals include humans, simians, farm animals, sport animals, rodents, and pets. The subject may be displaying a symptom(s) indicative of a health or physiological state or condition of the subject, such as a disease or disorder of the subject. As an alternative, the subject can be asymptomatic with respect to such health or physiological state or condition.

As used herein, the term “sample,” generally refers to a biological sample obtained from or derived from one or more subjects. Biological samples may be processed or fractionated before further analysis. Biological samples may include a whole blood (WB) sample, a PBMC sample, a tissue sample, a purified cell sample, or derivatives thereof. In some embodiments, a whole blood sample may be purified to obtain the purified cell sample. The term “derived from” used herein refers to an origin or source, and may include naturally occurring, recombinant, unpurified or purified molecules.

To obtain a blood sample, various techniques may be used, e.g., a syringe or other vacuum suction device. A blood sample can be optionally pre-treated or processed prior to use. A sample, such as a blood sample, may be analyzed under any of the methods and systems herein within 4 weeks, 2 weeks, 1 week, 6 days, 5 days, 4 days, 3 days, 2 days, 1 day, 12 hr, 6 hr, 3 hr, 2 hr, or 1 hr from the time the sample is obtained, or longer if frozen. When obtaining a sample from a subject (e.g., blood sample), the amount can vary depending upon subject size and the condition being screened. In some embodiments, at least 10 mL, 5 mL, 1 mL, 0.5 mL, 250, 200, 150, 100, 50, 40, 30, 20, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 μL of a sample is obtained. In some embodiments, 1-50, 2-40, 3-30, or 4-20 μL of sample is obtained. In some embodiments, more than 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 μL of a sample is obtained.

As used herein the term “diagnose” or “diagnosis” of a status or outcome includes predicting or diagnosing the status or outcome, determining predisposition to a status or outcome, monitoring treatment of patient, diagnosing a therapeutic response of a patient, and prognosis of status or outcome, progression, and response to particular treatment.

The sample may be taken before and/or after treatment of a subject with a disease or disorder. Samples may be obtained from a subject during a treatment or a treatment regime. Multiple samples may be obtained from a subject to monitor the effects of the treatment over time. The sample may be taken from a subject known or suspected of having a disease or disorder for which a definitive positive or negative diagnosis is not available via clinical tests. The sample may be taken from a subject suspected of having a disease or disorder. The sample may be taken from a subject experiencing unexplained symptoms, such as fatigue, nausea, weight loss, aches and pains, weakness, or bleeding. The sample may be taken from a subject having explained symptoms. The sample may be taken from a subject at risk of developing a disease or disorder due to factors such as familial history, age, hypertension or pre-hypertension, diabetes or pre-diabetes, overweight or obesity, environmental exposure, lifestyle risk factors (e.g., smoking, alcohol consumption, or drug use), or presence of other risk factors.

In some embodiments, a sample can be taken at a first time point and assayed, and then another sample can be taken at a subsequent time point and assayed. Such methods can be used, for example, for longitudinal monitoring purposes to track the development or progression of a disease. In some embodiments, the progression of a disease can be tracked before treatment, after treatment, or during the course of treatment, to determine the treatment's effectiveness. For example, a method as described herein can be performed on a subject prior to, and after, treatment with a disease state or condition therapy to measure the disease's progression or regression in response to the disease state or condition therapy.

After obtaining a sample from the subject, the sample may be processed to generate datasets indicative of a disease or disorder of the subject. For example, a presence, absence, or quantitative assessment of nucleic acid molecules of the sample at a panel of disease state or condition-associated or interferon-associated genomic loci or may be indicative of a disease state or condition of the subject. Processing the sample obtained from the subject may comprise (i) subjecting the sample to conditions that are sufficient to isolate, enrich, or extract a plurality of nucleic acid molecules, and (ii) assaying the plurality of nucleic acid molecules to generate the dataset (e.g., microarray data, nucleic acid sequences, or quantitative polymerase chain reaction (qPCR) data). Methods of assaying may include any assay known in the art or described in the literature, for example, a microarray assay, a sequencing assay (e.g., DNA sequencing, RNA sequencing, or RNA-Seq), or a quantitative polymerase chain reaction (qPCR) assay.

In some embodiments, a plurality of nucleic acid molecules is extracted from the sample and subjected to sequencing to generate a plurality of sequencing reads. The nucleic acid molecules may comprise ribonucleic acid (RNA) or deoxyribonucleic acid (DNA). The extraction method may extract all RNA or DNA molecules from a sample. Alternatively, the extraction method may selectively extract a portion of RNA or DNA molecules from a sample. Extracted RNA molecules from a sample may be converted to cDNA molecules by reverse transcription (RT).

The sample may be processed without any nucleic acid extraction. For example, the disease or disorder may be identified or monitored in the subject by using probes configured to selectively enrich nucleic acid (e.g., RNA or DNA) molecules corresponding to a panel of disease state or condition-associated or interferon-associated genomic loci. The probes may be nucleic acid primers. The probes may have sequence complementarity with nucleic acid sequences from one or more of the panel of disease state or condition-associated or interferon-associated genomic loci. The panel of disease state or condition-associated or interferon-associated genomic loci may comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, or more disease state or condition-associated or interferon-associated genomic loci.

The probes may be nucleic acid molecules (e.g., RNA or DNA) having sequence complementarity with nucleic acid sequences (e.g., RNA or DNA) of one or more genomic loci (e.g., disease state or condition-associated or interferon-associated genomic loci). These nucleic acid molecules may be primers or enrichment sequences. The assaying of the sample using probes that are selective for the one or more genomic loci (e.g., disease state or condition-associated or interferon-associated genomic loci) may comprise use of array hybridization, polymerase chain reaction (PCR), or nucleic acid sequencing (e.g., RNA sequencing or DNA sequencing, such as RNA-Seq).

The assay readouts may be quantified at one or more genomic loci (e.g., disease state or condition-associated or interferon-associated genomic loci) to generate the data indicative of the disease or disorder. For example, quantification of array hybridization or polymerase chain reaction (PCR) corresponding to a plurality of genomic loci (e.g., disease state or condition-associated or interferon-associated genomic loci) may generate data indicative of the disease or disorder. Assay readouts may comprise quantitative PCR (qPCR) values, digital PCR (dPCR) values, digital droplet PCR (ddPCR) values, fluorescence values, etc., or normalized values thereof.

Big Data Analysis Tools and Drug/Target Scoring Algorithms

The present disclosure provides systems and methods to perform data analysis using drug or target scoring algorithms and/or big data analysis tools. In various aspects, such drug or target scoring algorithms and/or big data analysis tools may be used to perform analysis of data sets including, for example, mRNA gene expression or transcriptome data, DNA genomic data, proteomic data, metabolomic data, other types of “-omic” data, or a combination thereof. Systems and methods of the present disclosure may use one or more of the following: a BIG-C™ big data analysis tool, an I-Scope™ big data analysis tool, a T-Scope™ big data analysis tool, a CellScan big data analysis tool, an MS (Molecular Signature) Scoring™ analysis tool, and a Gene Set Variation Analysis (GSVA) tool (e.g., P-Scope).

A method to assess a condition (e.g., COVID-19) of a subject may comprise using one or more data analysis tools and/or algorithms. The method may comprise receiving a dataset of a biological sample of a subject. Next, the method may comprise selecting one or more data analysis tools and/or algorithms. For example, the data analysis tools and/or algorithms may comprise a BIG-C™ big data analysis tool, an I-Scope™ big data analysis tool, a T-Scope™ big data analysis tool, a CellScan big data analysis tool, an MS (Molecular Signature) Scoring™ analysis tool, a Gene Set Variation Analysis (GSVA) tool (e.g., P-Scope), or a combination thereof. Next, the method may comprise processing the dataset using selected data analysis tools and/or algorithms to generate a data signature of the biological sample of the subject. Next, the method may comprise assessing the condition of the subject based on the data signature.

The BIG-C (Biologically Informed Gene Clustering) tool may be configured to sort large groups of genes into a set of functional groups (e.g., 53 functional groups). The functional groups are created utilizing publicly available information from online tools and databases including UniProtKB/Swiss-Prot, GO Terms, KEGG pathways, NCBI PubMed, and the Interactome. The functional groups may include one or more of: Active RNA, Anti-apoptosis, anti-proliferation, autophagy, chromatin remodeling, cytoplasm and biochemistry, cytoskeleton, DNA repair, endocytosis, endoplasmic reticulum, endosome and vesicles, fatty acid biosynthesis, cell surface, transcription, glycolysis and gluconeogenesis, golgi, immune cell surface, immune secreted, immune signaling, integrin pathway, interferon stimulated genes, intracellular signaling, lysosome, melanosome, MHC class I, MHC class II, microRNA processing, microRNA, mitochondrial transcription, mitochondria, mitochondria oxidative phosphorylation, mitochondrial TCA cycle, mRNA processing, mRNA splicing, non-coding RNA, nuclear receptor, nucleus and nucleolus, palmitoylation, pattern recognition receptors, peroxisomes, pro-apoptosis, pro-cell cycle, proteasome, pseudogenes, RAS superfamily, reactive oxygen species protection, secreted and extracellular matrix, transcription factors, transporters, transposon control, ubiquitylation and sumoylation, unfolded protein and stress, and unknown. Enrichment scores for each group are calculated based on an overlap p value to determine the functional groups over or under-expressed in the gene expression dataset. The BIG-C may be configured such that each gene is sorted into only one of the 53 functional groups, allowing for a quick and relatively simple understanding of types of genes enriched and co-expressed in a big dataset.

The I-Scope™ tool may be configured to identify immune infiltrates. Hematopoietic cells are unique in that they move throughout the body patrolling for threats to the host, and may infiltrate tissue sites not normally home to immune cells. I-Scope™ may be configured to identify hematopoietic cells through an iterative search of more than 17,000 genes identified in more than 50 microarray datasets. From this search, 1226 candidate genes are identified and researched for restriction in hematopoietic cells as determined by the HPA, GTEx and FANTOMS datasets (e.g., available at proteinatlas.org). 926 genes meet the criteria for being mainly restricted to hematopoietic lineages (brain, reproductive organ exclusions were permitted). These genes are researched for immune cell specific expression in 27 hematopoietic sub-categories: alpha beta T cell, T cell, regulatory T Cell, activated T cell, anergic T cell, gamma delta T cells, CD8 T, NK/NKT cell, NK cell, T & B cells, B cells, germinal center B cells, B cell and plasmacytoid dendritic cell, T &B & myeloid, B & myeloid, T & myeloid, MHC Class II expressing cell, monocyte, dendritic cell, plasmacytoid dendritic cells, myeloid cell, plasma cell, erythrocyte, neutrophil, low density granulocyte, granulocyte, and platelet. Transcripts are entered into I-Scope™ and the number of transcripts in each category determined. Odd's ratios are calculated with confidence intervals using the Fisher's exact test in R.

The T-Scope™ tool may be configured to help identify types of non-hematopoietic cells in gene expression datasets. T-Scope™ may be configured by downloading approximately 10,000 tissue enriched and 8,000 cell line enriched genes from the human protein atlas along with their tissue or cell line designation (e.g., available at proteinatlas.org). Genes found in more than four tissues are eliminated. Housekeeping genes described in the gene expression study by She et al. are also removed (e.g., as described by She et al., “Definition, conservation and epigenetics of housekeeping and tissue-enriched genes,” BMC Genomics 2009, 10:269, which is incorporated herein by reference in its entirety). This list is further curated by removing genes differentially expressed in 34 hematopoietic cell gene expression datasets and adding kidney specific genes from datasets downloaded from the GEO repository and processed by Ampel BioSolutions. The resulting categories of genes represent genes enriched in the following 42 tissue/cell specific categories: adrenal gland, breast, cartilage, cerebral cortex, uterine cervix, chondrocyte, colon, duodenum, endometrium, epididymis, esophagus fallopian tube, esophagus, fibroblast, heart muscle, keratinocyte, kidney, liver, lung, melanocyte, ovary pancreas, parathyroid gland, placenta, podocyte, prostrate, rectum, salivary gland, seminal vesicle, skeletal muscle, skin, small intestine, smooth muscle, stomach, synoviocyte, testis, kidney loop of henle, kidney proximal tubule, kidney distal tubule, and kidney collecting duct.

The CellScan tool may be a combination of I-Scope™ and T-Scope™, and may be configured to analyze tissues with suspected immune infiltrations that should also have tissue specific genes. CellScan may potentially be more stringent than either I-Scope™ or T-Scope™ because it may be used to distinguish resident tissue cells from non-resident hematopoietic cells.

The MS (Molecular Signature) Scoring tool may be configured to assess specific pathways in a disease state. Information on genes that encode for proteins that participate in a specific signaling pathway, and whether the gene product promotes or inhibits the pathway, are compiled and curated through literature mining. Curated pathways presented by the company include CD40-CD40ligand, IL-6, IL-12/23, TNF, IL-17, IL-21, S1P1, IL-13 and PDE4, but this method may be used for any known signaling pathway with available data. To determine if a signaling pathway is over or under-expressed in a microarray dataset, the gene list for each signaling pathway may be queried against the limma differentially expressed genes from a disease state compared to healthy controls, and the differentially expressed genes in the signaling pathway may be identified for each set. The fold changes for genes that promoted the pathway may be added together and the fold changes for genes that inhibited the pathway may be subtracted from the score. This total score may be normalized based on the number of genes that could be detected on the specific microarray platform used for the experiment. Activation scores of −100 to +100 may be determined using this method with negative scores indicating an inhibition of the specific pathway in the disease state and positive scores indicating an up-regulation of a specific pathway in the disease state. The Fischer's exact test may be performed to determine if there was sufficient overlap of genes between the experimental differentially expressed genes and the genes in the signaling pathway.

Gene Set Variation Analysis (GSVA) may be performed (for example, as described in Catalina et al. (2019, Communications Biology, “Gene expression analysis delineates the potential roles of multiple interferons in systemic lupus erythematosus”, which is incorporated herein by reference in its entirety) to determine enrichment of signaling pathways in individual patient samples. Gene set variation analysis may be performed using an open source software package for the coding language R available at the R Bioconductor (bioconductor.org), e.g., as described by Hanzelman et al., (“GSVA: gene set variation analysis for microarray and RNA-Seq data,” BMC Bioinformatics, 2013, which is incorporated herein by reference in its entirety). The modules of genes to interrogate the datasets may be developed. Modules of genes determined to represent a specific signaling pathway or process may be identified (e.g., using publicly available datasets). For example, the IFNB1 signaling pathway is taken from a publicly available gene expression dataset of peripheral blood cells treated with IFNB1 in vitro. Genes co-expressed in this dataset (genes either all increased or decreased compared to control treated peripheral blood) are used to create modules of genes representing the IFNB1 signaling pathway, and GSVA is used to determine the enrichment of this set of genes and hence the IFNB1 signaling pathway in individual patient and control samples.

BIG-C™ Big Data Analysis Tool

BIG-C® is a fast and efficient cloud-based tool to functionally categorize gene products. With coverage of over 80% of the genome, BIG-C® leverages publicly available databases such as UniProtKB/Swiss-Prot, GO terms, KEGG pathways, NCBI PubMed and Interactome to place genes into 53 functional categories. The sorting into only one of 53 functional groups allows for a quick and relatively simple understanding of types of genes enriched and co-expressed in a big dataset. This assists in deriving further insights from genes expressed for a given disease state in human or pre-clinical mouse models.

BIG-C® can be used to functionally categorize immunological genes that are not covered in cancer databases such as GO and KEGG (e.g., as described by Grammer et al. 2016, “Drug repositioning in SLE: crowd-sourcing, literature-mining and Big Data analysis,” Lupus, 25 (10), 1150-1170, which is incorporated herein by reference in its entirety). Using a knowledge base of over 5000 patients with systemic lupus erythematosus (SLE), over 16432 genes may be each placed into one of 53 BIG-C® functional categories, and statistical analysis may be performed to identify enriched categories. BIG-C® categories may be cross-examined with the GO and KEGG terms to obtain additional information and insights.

A sample BIG-C® workflow may comprise the following steps. First, SLE genomic datasets are derived from whole blood, peripheral blood mononuclear cells, affected tissues, and purified immune cells. Second, datasets are analyzed using DE analysis or Weighted Gene Coexpression Network Analysis (WGCNA). Third, expressed genes are annotated using publicly available databases (e.g., UniProtKB/Swiss-Prot database, Human Immunodeficiencies database, Mouse MGI database, Entrez Molecular Sequence database, PubMed, and the Human Tissue Atlas). Fourth, signatures are cross-referenced with purified single-cell microarray datasets and RNAseq experiments. Fifth, BIG-C® is leveraged to separate the individual annotated genes into one of 53 functional categories shown in Table 1 (e.g., as described by Labonte et al. 2018, “Identification of alterations in macrophage activation associated with disease activity in systemic lupus erythematosus,” PloS one, 13 (12), e0208132, which is incorporated herein by reference in its entirety). Sixth, chi-squared analysis is used to determine enriched categories of interest from overlap p-values. Seventh, enriched categories are cross-examined with GO and KEGG terms to derive key insights for further analysis.

TABLE 1 BIG-C Categories Immune Cell General Cell Immune Intracellular MHC Class MHC Class Secreted Pat. Recog. Surface Surface Signaling Signaling I II Immune Secreted ECM Receptors Interferon PRO-Cell Anti-Cell PRO Anti Unfold Prot. Proteasome Autophagy Ubiquity lation Gene Sig Cycle Cycle Apoptosis Apoptosis Stress General Transcript. Nuc Chromatin DNA mRNA mRNA MicroRNA Cytoskeleton Transcript. Factors Horm. Remodel Repair Translation Splicing Processing Receptors Integrin RAS WNT Lysosome Endocytosis Endosome Endoplas. Oxidative TCA Cycle Pathway Superfamily Signaling & Vesicles Retic. Phosphor. Mito. DNA Mito FA Transporters Cytoplasm Peroxisomes ROS Nuclear & Active RNA toRNA Biosynth Biochem Protection Nucleolus MicroRNA Melanosome Unknown Pseudogenes Transposon Golgi Glycolysis Palmitoylation Control

I-Scope™ Big Data Analysis Tool

I-Scope™ may be a tool configured for cross-examining the presence and activity of varying types of immune cell infiltrates with observed gene expression patterns. It may take annotated gene expression data and analyze it for hematopoietic cell lineage. I-Scope™ can be used downstream of the BIG-C® (Biologically Informed Gene-Clustering) tool in that it helps to provide even more insight into the nature of the genes being expressed after categorization.

I-Scope™ addresses the need to understand the involvement of specific cells for a given disease state. While it is helpful to understand the relative up-regulation and down-regulation at the gene expression level, it is even more informative to understand specifically in which cells this is occurring. I-Scope™ may be configured to identify hematopoietic cells through an iterative search of more than 17,000 genes identified in more than 50 microarray datasets (e.g., as described by Hubbard et al., “Analysis of Lupus Synovitis Gene Expression Reveals Dysregulation of Pathogenic Pathways Activated within Infiltrating Immune Cells,” Arthritis Rheumatol, 2018; 70 (suppl 10), which is incorporated herein by reference in its entirety). I-Scope™ may function by restricting the analysis to genes of hematopoietic cell heritage and allow for cross-checking against purified single-cell experiments or datasets. The cross-check confirms and categorizes specific transcript signatures to the 28 hematopoietic cell sub-categories shown in Table 2, ultimately allowing for cellular activity analysis across multiple samples and disease states. When combined with BIG-C® categories, the cellular activity can be correlated to specific functions within a given cell type.

TABLE 2 I-Scope™ Cell Sub-Categories Monos/ Plasma Macs Cells T-Cells B-Cells Dendritic T&B Cells CD8 T Myeloid Tact LDG Hematopoietic Neutrophil Ag Granulocytes Cells Presentation Platelets pDC T, B, Mono Langerhans Bact Mono and Erythrocytes B Mast Cell T reg Gd T T anergic FDC CD4T T/NK/NKT Cells

A sample I-Scope™ workflow may comprise the following steps. First, candidate genes are identified from datasets (associated with a disease state or condition) potentially associated with immune cell expression. Second, using HPA, GTEx, and FANTOMS datasets, expression signatures associated with hematopoietic cell lineage are identified. Third, signatures are cross-referenced with purified single-cell microarray datasets and RNAseq experiments. Fourth, transcripts are categorized into 28 hematopoietic cell sub-categories and assess cellular expression across different samples and disease states. Odd's ratios are calculated with confidence intervals using the Fisher's exact test in R. An I-Scope™ signature analysis for a given sample may lead to the I-Scope™ signature analysis across multiple samples and disease states.

T-Scope™ Big Data Analysis Tool

The T-Scope™ tool may be configured for cross-examining gene expression signatures of a given sample with a database of non-hematopoietic cell types (e.g., as described by Hubbard et al., “Analysis of Gene Expression from Systemic Lupus Erythematosus Synovium Reveals Unique Pathogenic Mechanisms [Abstract], Annual Meeting of the American College of Rheumatology; June 2019; Chicago, Ill., which is incorporated herein by reference in its entirety). T-Scope™ may comprise a database of 704 transcripts allocated to 45 independent categories. Transcripts detected in the sample are matched to one of the cellular categories within the T-Scope™ tool to derive further insights on tissue cell activity. T-Scope™ can be used downstream of the BIG-C® (Biologically Informed Gene-Clustering) tool to understand which tissue cell types are present. In conjunction with I-Scope™ (which provides information related to immune cells), T-Scope™ can be performed to provide a complete view of all possible cell activity in a given sample.

T-Scope™ addresses the need to understand the involvement of specific tissue cells for a given disease state. While it is helpful to understand the relative up-regulation and down-regulation at the gene expression level, it is even more informative to understand specifically in which cells this is occurring. T-Scope™ may be configured by downloading a set of approximately 10,000 tissue enriched and 8,000 cell line enriched genes from the Human Protein Atlas along with their tissue or cell line designation. Genes differentially expressed in hematopoietic cell datasets are removed and kidney specific genes are added from the GEO repository. T-Scope™ may function by restricting the analysis to genes of known tissue cell heritage and allow for cross-checking against purified single-cell experiments or datasets. The cross-check confirms and categorizes specific transcript signatures to the 45 tissue cell sub-categories (as shown in Table 3), ultimately allowing for cellular activity analysis across multiple samples and disease states. When combined with BIG-C® categories, the cellular activity can be correlated to specific functions within a given tissue cell type.

TABLE 3 T-Scope™ 45 Categories of Tissue Cells Adipose Adrenal Cerebral Cervix, Tissue Gland Breast Cartilage Cortex Uterine Chondrocyte Colon Dendritic Duodenum Endometrium Endothelial Epididymis Erythrocytes Esophagus Fallopian Fibroblast Gallbaldder Tube Heart Muscle Keratinocyte Keratinocyte Kidney Kidney Kidney Loop Kidney Kidney Kidney Skin Distal Proximal Tubule Duct Tubule Tubules Tubules Langherhans Liver Lung Melanocyte Podocyte Prostate Rectum Salivary Seminal Gland Vesicle Skeletal Skin Small Smooth Stomach Synoviocyte Testis Thyroid Urinary Muscle Intenstine Muscle Gland Bladder

A sample T-Scope™ workflow may comprise the following steps. First, candidate genes are identified from differential expression datasets (associated with a disease state or condition) potentially associated with tissue cell expression. Second, using publicly available databases, expression signatures associated with potential tissue cell activity are identified. Third, signatures are cross-referenced with microarray, scRNAseq or RNAseq experiments. Fourth, transcripts are categorized into 45 tissue cell sub-categories and cellular expression is assessed across different samples and disease states. Results may be obtained using T-Scope™ in combination with I-Scope™ for identification of cells post-DE-analysis.

Cell Scan Big Data Analysis Tool

A cloud-based genomic platform may be configured to provide users with access to CellScan™, which comprises a suite of tools for the identification, analysis, and prioritization of targets for drug development and/or repositioning. This platform is powered by a database containing the genomic information gathered from 5000+ autoimmune patients. The cloud-based genomic platform may leverage results from RNAseq and microarray experiments in conjunction with clinical information, such as medication and lab tests, to provide previously undiscovered insights.

CellScan™ may go beyond typical ‘omics analysis by performing one or more of the following: functionally categorizing genes and their products (e.g., using BIG-C®); deconvolving gene expression data to identify unique immunological cell types from blood or biopsy samples (e.g., using I-Scope™); identifying tissue specific cell from biopsy samples (e.g., using T-Scope™); identifying receptor-ligand interactions and subsequent signaling pathways (e.g., using MS-Scoring™); ranking genes and their products for targeting by drugs and miRNA mimetics; and prioritizing FDA-approved drugs and drugs-in-development for treatment in patients or pre-clinical models.

CellScan™ applications may include one or more of: Biomarker Discovery, Disease Mechanisms, Drug Mechanism of Action, Drug Mechanism of Toxicity, and Target Identification and Validation. Experimental approaches supported by CellScan™ may include one or more of: lncRNA, Metabolomics, MicroArray, miRNA, mRNA, qPCR, Proteomics, and RNAseq.

Data analysis and interpretation with CellScan™ may build on comprehensive, manually curated content of a knowledge base. Powerful, quick, and efficient tools may be used to perform deep analysis of NGS and miRNA data to identify gene function, immunological and tissue cell type, pathways, and target/drug appropriate for a specific disease state.

CellScan™ features may be configured to optimize or maximize the impact of information that surfaces in an analysis so that interpretation of a dataset is comprehensive and elucidates actionable insights. These features may include one or more of: NGS RNAseq data analysis, biomarker scoring, and prioritizing targets and drugs for human clinical trials and/or pre-clinical models. The NGS RNAseq data analysis may comprise interrogating RNA and miRNA data for function, cell-type (immunological or tissue) and pathways. The biomarker scoring may comprise using a knowledge base and gene expression data to assess and prioritize biomarkers associated with a target disease or phenotype. The target/drug prioritization may comprise leveraging objective scoring of targets and drugs based on parameters such as scientific rationale, evidence in mouse/human cells, prior clinical data, overall drug properties, and the risk of adverse events.

The knowledge base may be a repository created from millions of individual pieces of information gathered about genes, cells, tissues, drugs, and diseases, and manually reviewed for accuracy and includes rich contextual details and links to original publications. The knowledge base may enable access to relevant and substantiated knowledge from primary literature as well as public and private databases for comprehensive interpretation of NGS/RNAseq data elucidating function/pathways and prioritize targets/drugs for given disease states. Table 4 shows an example list of reference databases for the content in CellScan™, with both human and mouse species-specific identifiers supported.

TABLE 4 Reference Databases for Content in CellScan ™ Affymetrix Entrez Gene HPA scRNAseq Agilent FANTOM5 Illumina STITCH BrainArray GenBank Interactome Mouse Genome Database (MGD) CAS Registry Gene Symbol-human KEGG UCSC Number (Hugo/HGNC) (hg 18) Clinicaltrials.gov Gene Symbol-mouse LINCS/CLUE UCSC (Entrez Gene) (hg 19) CodeLink GNF Tissue Mosby's Drug Unigene Expression Body Consult Atlas DrugBank GO terms NCBI PubMed Uniprot/ Swiss-Prot Accession Drugs@FDA Goodman & Gilman's NCI-60 Cell Line Pharmacological Basis Expression Atlas of Therapeutics Ensembl GTEx Refseq

MS (Molecular Signature) Scoring™ Analysis Tool

MS-Scoring™ may be configured to identify receptor-ligand interactions and predict ongoing signaling pathways. In addition, MS-Scoring™ may be used to validate molecular pathways as potential targets for new or repurposed drug therapies. The specificity of next-generation drug therapies requires a way to understand the potential of a given therapy to act on the intended biochemical target. Moreover, a potential application of this is the repositioning of drug therapies that may have the correct biochemical targeting to address multiple clinical needs beyond the initial intended therapeutic value.

MS-Scoring™ may be specifically developed to address gaps in the QIAGEN IPA® (Ingenuity Pathway Analysis) tool that does not contain many immunologically relevant pathways. Similar to IPA®, MS-Scoring™ 1 may use log-fold change information to score the target and its signaling pathway to verify the viability of the targets. If the fold-change of the genes of a signaling pathway appears to be upregulated or inhibitors appear to be downregulated, MS-Scoring™ 1 may provide a score of +1. Conversely if the genes of a signaling pathway appear downregulated or the inhibitors upregulated, MS-Scoring™ 1 may provide a score of −1. A score of zero may be provided if no fold-change is observed. The scores may then be summed and normalized across the entire pathway to yield a final % score between −100 (inhibition) and +100 (up-regulation). Higher absolute magnitude scores, scores that are close to −100 or +100, may indicate a high potential for therapeutic targeting. The Fischer's exact test may be performed to determine if there is sufficient overlap of genes between the experimental differentially expressed genes and the genes in the signaling pathway.

A sample MS-Scoring™ 1 workflow may comprise the following steps. First, potential drugs and pathways are identified by LINCS (Library of Integrated Network-Based Cellular Signatures) as candidates for therapeutic intervention. Second, MS-Scoring™ 1 is used to evaluate individual transcript elements of the target pathway. Third, signatures are cross-referenced with purified single-cell microarray datasets and RNAseq experiments. Fourth, scores are compiled and normalized to provide an overall % score for the pathway and higher absolute magnitude scores indicate a higher potential for therapeutic targeting.

MS-Scoring™ 2 may utilize custom-defined gene modules that represent a signaling pathway or process and is particularly useful for gene expression datasets from microarray or RNAseq. The MS-Scoring™ 2 tool may be configured to take a deeper look at signaling pathways analyzed using the MS-Scoring™ 1. The tool may analyze raw gene expression data and assess enrichment by the Gene Set Variation Analysis (as described herein), which assigns an indexed score to the individual co-expressed pathways between −1 and +1 indicating levels of down-regulation and up-regulation respectively.

A sample MS-Scoring™ 2 workflow may comprise the following steps. First, a signaling pathway of interest is selected from the MS-Scoring™ 2 menu. Second, a raw gene expression data is inputted into the MS-Scoring™ 2 tool. Third, enrichment of signaling pathway (s) is assessed on a patient by patient basis. Fourth, the data can then be used to drive insight for the target signaling pathways in individual patient samples.

Gene Set Variation Analysis (GSVA)

Gene Set Variation Analysis (GSVA) algorithms may be performed (for example, as described in Catalina et al. (2019, Communications Biology, “Gene expression analysis delineates the potential roles of multiple interferons in systemic lupus erythematosus”, which is incorporated herein by reference in its entirety) to determine enrichment of signaling pathways in individual patient samples. Gene set variation analysis may be performed using an open source software package for the coding language R available at the R Bioconductor (bioconductor.org), e.g., as described by Hanzelman et al., (“GSVA: gene set variation analysis for microarray and RNA-Seq data,” BMC Bioinformatics, 2013, which is incorporated herein by reference in its entirety) and as described by [R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. www.R-project.org/], which is incorporated herein by reference in its entirety. The modules of genes to interrogate the datasets may be developed. Modules of genes determined to represent a specific signaling pathway or process may be identified (e.g., using publicly available datasets). For example, the IFNB1 signaling pathway is taken from a publicly available gene expression dataset of peripheral blood cells treated with IFNB1 in vitro. Genes co-expressed in this dataset (genes either all increased or decreased compared to control treated peripheral blood) are used to create modules of genes representing the IFNB1 signaling pathway, and GSVA is used to determine the enrichment of this set of genes and hence the IFNB1 signaling pathway in individual patient and control samples.

A GSVA-based data analysis tool may be developed for use in analyzing specific sets of gene pathways. The GSVA-based data analysis tool (e.g., P-Scope) may use a GSVA statistical test-based tool using different sets of genes to analyze certain pathways. Such sets of genes may include, for example, human genes, mouse genes, or a combination thereof.

Computer Systems

The present disclosure provides computer systems that are programmed to implement methods of the disclosure. FIG. 16 shows a computer system 1601 that is programmed or otherwise configured to, for example, perform methods of the disclosure.

The computer system 1601 can regulate various aspects of analysis, calculation, and generation of the present disclosure, such as, for example, performing methods of the disclosure. The computer system 1601 can be an electronic device of a user or a computer system that is remotely located with respect to the electronic device. The electronic device can be a mobile electronic device.

The computer system 1601 includes a central processing unit (CPU, also “processor” and “computer processor” herein) 1605, which can be a single core or multi core processor, or a plurality of processors for parallel processing. The computer system 1601 also includes memory or memory location 1610 (e.g., random-access memory, read-only memory, flash memory), electronic storage unit 1615 (e.g., hard disk), communication interface 1620 (e.g., network adapter) for communicating with one or more other systems, and peripheral devices 1625, such as cache, other memory, data storage and/or electronic display adapters. The memory 1610, storage unit 1615, interface 1620 and peripheral devices 1625 are in communication with the CPU 1605 through a communication bus (solid lines), such as a motherboard. The storage unit 1615 can be a data storage unit (or data repository) for storing data. The computer system 1601 can be operatively coupled to a computer network (“network”) 1630 with the aid of the communication interface 1620. The network 1630 can be the Internet, an internet and/or extranet, or an intranet and/or extranet that is in communication with the Internet.

The network 1630 in some cases is a telecommunication and/or data network. The network 1630 can include one or more computer servers, which can enable distributed computing, such as cloud computing. For example, one or more computer servers may enable cloud computing over the network 1630 (“the cloud”) to perform various aspects of analysis, calculation, and generation of the present disclosure, such as, for example, performing methods of the disclosure. Such cloud computing may be provided by cloud computing platforms such as, for example, Amazon Web Services (AWS), Microsoft Azure, Google Cloud Platform, and IBM cloud. The network 1630, in some cases with the aid of the computer system 1601, can implement a peer-to-peer network, which may enable devices coupled to the computer system 1601 to behave as a client or a server.

The CPU 1605 may comprise one or more computer processors and/or one or more graphics processing units (GPUs). The CPU 1605 can execute a sequence of machine-readable instructions, which can be embodied in a program or software. The instructions may be stored in a memory location, such as the memory 1610. The instructions can be directed to the CPU 1605, which can subsequently program or otherwise configure the CPU 1605 to implement methods of the present disclosure. Examples of operations performed by the CPU 1605 can include fetch, decode, execute, and writeback.

The CPU 1605 can be part of a circuit, such as an integrated circuit. One or more other components of the system 1601 can be included in the circuit. In some cases, the circuit is an application specific integrated circuit (ASIC).

The storage unit 1615 can store files, such as drivers, libraries and saved programs. The storage unit 1615 can store user data, e.g., user preferences and user programs. The computer system 1601 in some cases can include one or more additional data storage units that are external to the computer system 1601, such as located on a remote server that is in communication with the computer system 1601 through an intranet or the Internet.

The computer system 1601 can communicate with one or more remote computer systems through the network 1630. For instance, the computer system 1601 can communicate with a remote computer system of a user. Examples of remote computer systems include personal computers (e.g., portable PC), slate or tablet PC's (e.g., Apple® iPad, Samsung® Galaxy Tab), telephones, Smart phones (e.g., Apple® iPhone, Android-enabled device, Blackberry®), or personal digital assistants. The user can access the computer system 1601 via the network 1630.

Methods as described herein can be implemented by way of machine (e.g., computer processor) executable code stored on an electronic storage location of the computer system 1601, such as, for example, on the memory 1610 or electronic storage unit 1615. The machine executable or machine-readable code can be provided in the form of software. During use, the code can be executed by the processor 1605. In some cases, the code can be retrieved from the storage unit 1615 and stored on the memory 1610 for ready access by the processor 1605. In some situations, the electronic storage unit 1615 can be precluded, and machine-executable instructions are stored on memory 1610.

The code can be pre-compiled and configured for use with a machine having a processor adapted to execute the code, or can be compiled during runtime. The code can be supplied in a programming language that can be selected to enable the code to execute in a pre-compiled or as-compiled fashion.

Aspects of the systems and methods provided herein, such as the computer system 1601, can be embodied in programming. Various aspects of the technology may be thought of as “products” or “articles of manufacture” typically in the form of machine (or processor) executable code and/or associated data that is carried on or embodied in a type of machine-readable medium. Machine-executable code can be stored on an electronic storage unit, such as memory (e.g., read-only memory, random-access memory, flash memory) or a hard disk. “Storage” type media can include any or all of the tangible memory of the computers, processors or the like, or associated modules thereof, such as various semiconductor memories, tape drives, disk drives and the like, which may provide non-transitory storage at any time for the software programming. All or portions of the software may at times be communicated through the Internet or various other telecommunication networks. Such communications, for example, may enable loading of the software from one computer or processor into another, for example, from a management server or host computer into the computer platform of an application server. Thus, another type of media that may bear the software elements includes optical, electrical and electromagnetic waves, such as used across physical interfaces between local devices, through wired and optical landline networks and over various air-links. The physical elements that carry such waves, such as wired or wireless links, optical links or the like, also may be considered as media bearing the software. As used herein, unless restricted to non-transitory, tangible “storage” media, terms such as computer or machine “readable medium” refer to any medium that participates in providing instructions to a processor for execution.

Hence, a machine-readable medium, such as computer-executable code, may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium or physical transmission medium. Non-volatile storage media include, for example, optical or magnetic disks, such as any of the storage devices in any computer(s) or the like, such as may be used to implement the databases, etc. shown in the drawings. Volatile storage media include dynamic memory, such as main memory of such a computer platform. Tangible transmission media include coaxial cables; copper wire and fiber optics, including the wires that comprise a bus within a computer system. Carrier-wave transmission media may take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (IR) data communications. Common forms of computer-readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD-ROM, any other optical medium, punch cards paper tape, any other physical storage medium with patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer may read programming code and/or data. Many of these forms of computer-readable media may be involved in carrying one or more sequences of one or more instructions to a processor for execution.

The computer system 1601 can include or be in communication with an electronic display 1635 that comprises a user interface (UI) 1640 for providing, for example, a visual display. Examples of UIs include, without limitation, a graphical user interface (GUI) and web-based user interface.

Methods and systems of the present disclosure can be implemented by way of one or more algorithms. An algorithm can be implemented by way of software upon execution by the central processing unit 1605. The algorithm can, for example, perform methods of the disclosure.

EXAMPLES

The following illustrative examples are representative of embodiments of the software applications, systems, and methods described herein and are not meant to be limiting in any way.

Example 1: Comprehensive Gene Expression Analysis Reveals Targetable Pathologic Processes in Blood, Lung, and Airway of COVID-19 Patients

Abstract

SARS-CoV2 is a previously uncharacterized coronavirus and causative agent of the COVID-19 pandemic. COVID-19 typically causes mild respiratory symptoms, but may escalate to acute respiratory distress syndrome (ARDs) with an increased risk of respiratory failure and death. However, the trajectory of disease progression and the status of affected tissues in COVID-19 patients has not been elucidated. We performed a comprehensive analysis of gene expression data from the blood, lung, and airway of COVID-19 patients to better understand the host response to SARS-CoV2 infection. Our results indicate that COVID-19 pathogenesis is driven by populations of myeloid-lineage cells with highly inflammatory but distinct transcriptional signatures, suggesting a progression in activation from the periphery to the lung tissue. In addition, through analysis of immune cells and inflammatory pathways enriched in each compartment, we have built a model of the systemic response to SARS-CoV2 and identified therapeutics targeting key upstream regulators of pathways contributing to COVID-19 pathogenesis.

Introduction

Coronaviruses (CoV) are a group of enveloped single positive stranded RNA viruses named for the spike proteins on their surface that resemble a crown (Fung and Liu, 2019). Seven coronaviruses have now been found to infect humans, causing mild to severe respiratory and intestinal illnesses including an estimated 15% of common colds (Cui et al., 2019; Greenberg, 2016). In the past two decades, three global pandemics have originated from coronaviruses capable of infecting the lower respiratory tract resulting in heightened pathogenicity and high mortality rates in humans. In 2002-2003, severe acute respiratory syndrome coronavirus (SARS-CoV) lead to greater than 8,000 cases with a mortality rate of nearly 10% (Drosten et al., 2003; Fung and Liu, 2019). Subsequently, Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in 2012, leading to over 2,000 confirmed cases and a mortality rate of approximately 35% (Chafekar and Fielding, 2018; Fung and Liu, 2019). We are currently in the midst of a pandemic stemming from a new coronavirus strain, severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the causative agent of coronavirus disease 2019 (COVID-19). In the majority of cases, patients exhibit mild symptoms, whereas in more severe cases, patients may develop acute respiratory distress syndrome (ARDS), which leads to lung injury and death from respiratory failure (Chen et al., 2020a; Zhang et al., 2020).

SARS-CoV2 utilizes the SARS-CoV receptor, ACE2, in conjunction with the spike protein activator, TMPRSS2, to infect host cells (Hoffmann et al., 2020). Expression of ACE2 and TMPRSS2 has been detected in multiple tissues including lung epithelium and vascular endothelium, (Lovren et al., 2008; Sungnak et al., 2020) which are likely to be the first cells infected by the virus. However, at this time, there is still incomplete information available regarding the host response to SARS-CoV2 infection and the perturbations resulting in a severe outcome. Despite this, clues can be derived from our knowledge of the immune response to infection by other respiratory viruses, including SARS-CoV and MERS-CoV. After infection, viruses are typically detected by pattern recognition receptors (PRRs) such as the inflammasome sensor NLRP3, which signal the release of interferons and inflammatory cytokines including the IL-1 family, IL-6, and TNF which activate a local and systemic response to infection (Kelley et al., 2019; Lazear et al., 2019). This involves the recruitment, activation, and differentiation of innate and adaptive immune cells including neutrophils, inflammatory myeloid cells, CD8 T cells, and natural killer (NK) cells (Newton et al., 2016). Resolution of infection is largely dependent on the cytotoxic activity of CD8 T cells and NK cells, which enables clearance of virus-infected cells and thus acts to prevent further spread of the virus (Newton et al., 2016). Failure to clear virus-infected cells may facilitate a hyper-inflammatory state termed “cytokine storm”, macrophage activation syndrome (MAS), or haemophagocytic lymphohystocytosis (HLH) and ultimately damage to the infected lung (Crayne et al., 2019; McGonagle et al., 2020). Clearance of virus also coincides with development of neutralizing antibodies, although recent studies have suggested that 30% of subjects who clear SARS-CoV2 do not develop neutralizing antibodies (Tay et al.). Moreover, the role of the anti-SARS-CoV2 antibody is complex, in that in non-human primates, anti-viral antibody may exacerbate the lung pathology, a phenomenon also reported in older subjects infected with the virus (Wang et al., 2020).

The novelty of SARS-CoV2 and thus the lack of comprehensive knowledge regarding the progression of COVID-19 disease, has constrained our ability to develop effective treatments for infected patients. One means to obtain a comprehensive knowledge of the host response to SARS-CoV2 is to examine gene expression in relevant tissues. A limited number of studies have been reported and have suggested that the disease generally induces a dysfunctional immune response involving lymphopoenia, increased inflammatory cell recruitment to the lung, and an increase in local and systemic release of pro-inflammatory cytokines or “cytokine storm”, conditions which are exacerbated in more severe cases (Tay et al.). However, because of the small number of samples and limited analysis, a full picture of the biological state of SARS-CoV2-affected tissues has not emerged. To address this, we have assessed all of the available SARS-CoV2 gene expression datasets using a number of orthogonal bioinformatic tools to better understand the host response to SARS-CoV2 infection. As a result, we have identified immune cell types and inflammatory pathways critical for COVID-19 pathogenesis. Furthermore, we have characterized differences in transcriptional signatures between these compartments to develop a model for the systemic response to SARS-CoV2 infection and identified potential drugs to target harmful inflammatory mediators in COVID-19 patients.

Results

Gene Expression Analysis of Blood, Lung, and Airway of COVID-19 Patients

Gene expression reflects the current state of cellular activity of cells or organs and can be employed to delineate changes in cellular composition and/or function in a sample. A limited number of gene expression profiles are available from patients with COVID-19 and have yielded some insights into the pathogenic processes triggered by infection with SARS-CoV-2 (Blanco-Melo et al., 2020; Wei et al., 2020; Xiong et al., 2020). We reasoned that a more comprehensive analysis of all available gene sets from blood, lung and airway using a number of complementary orthogonal approaches might provide a more complete view of the nature of the COVID-19 inflammatory response and the potential points of intervention that might have therapeutic value. To characterize the pathologic response to SARS-CoV2 infection manifested in the peripheral blood and lung of COVID-19 patients, we analyzed RNA sequencing (RNA-seq) data from peripheral blood mononuclear cells (PBMCs) and postmortem lung tissue of COVID-19 patients and healthy controls as well as bronchoalveolar lavage (BAL) fluid of COVID-19 patients (Blanco-Melo et al., 2020; Xiong et al., 2020). We first determined changes in gene expression in the blood (PBMC-CTL vs PBMC-CoV2) and lung (Lung-CTL vs Lung-CoV2). Because no control BAL fluids were associated with the BAL-CoV2 samples, we compared BAL-CoV2 to PBMC-CoV2 from the same dataset to avoid effects related to batch and methodology. These results must be viewed with caution, understanding that the comparison can only show changes in gene expression profiles between different compartments. Despite that, important differences were observed. Overall, we found 4,277 differentially expressed genes (DEGs) in the blood (2,175 up and 2,102 down), 2,261 DE genes in the lung (711 up and 1550 down), and 9,183 DE genes in the airway (4,263 up and 4,920 down). From these comparisons, we traced transcriptional changes in the progression of the pathologic response to SARS-CoV2 through these three compartments from activation and mobilization of immune cells in the blood, to infiltration into the lung tissue and airway of infected patients (FIG. 1A).

Conserved and Differential Enrichment of Immune Cells and Pathways in Blood, Lung, and Airway of COVID-19 Patients

To interrogate pathologic pathways in the 3 compartments, we performed Gene Set Variation Analysis (GSVA) utilizing previously reported interferon response gene (IRG) modules (Catalina et al., 2019), gene modules of inflammatory pathways curated from online databases, and previously defined gene modules characterizing immune and inflammatory cells and processes (Cataline et al. unpublished manuscript) (FIG. 8 ). This analysis allowed us to identify differences in inflammatory pathways and immune cell types enriched in COVID-19 patients as compared to healthy controls as well those that were differentially enriched between the blood, lung, and airway compartments. Overall, our results revealed increased inflammatory pathway signatures (FIG. 1B), decreased lymphoid cell signatures (FIG. 1C), and increased myeloid cell signatures (FIG. 1D) in COVID-19 patients, a pattern that is consistent with earlier studies (Blanco-Melo et al., 2020; Wen et al., 2020; Xiong et al., 2020). Interestingly, we found important differences in the gene expression profiles between the blood, lung, and airway compartments.

In the blood, inflammatory pathways including the classical and lectin-induced complement pathways and the NLRP3 inflammasome were enriched (FIG. 1B). T cells were significantly decreased in the blood of 2 out of 3 COVID-19 patients and cytotoxic CD8 T cells and NK cells were significantly decreased in all patients. In contrast, we found enrichment of signatures for the CD40 activated pathway and plasma cells only in the blood and not the lung or airway of infected individuals (FIG. 1C). Myeloid populations, which include monocytes and granulocytes, were not enriched in the blood of COVID-19 patients compared to controls (FIG. 1D). However, we did observe a significant increase in the monocyte-specific gene signature as well as polarized M1/M2 macrophages (FIG. 1D).

Although, there is conflicting data on the presence of an Interferon Gene Signature (IGS) and whether SARS-CoV2 infection induces a robust IFN response, (Blanco-Melo et al., 2020) we observed increased expression of Type I interferon genes (IFNA4, IFNA6, IFNA10) and significant enrichment of the Type I and Type II IGS specifically in the lung tissue, but not in the blood or airway of COVID-19 patients (FIG. 7 ; FIG. 1B). We also observed enrichment of other potentially pathologic processes in the lung that were shared with the other compartments, including the classical and alternative complement pathways and NLRP3 inflammasome signatures (FIG. 1B). In the lung tissue, overall T cell signatures were modestly, but not significantly enriched, and activated or cytotoxic cells were not enriched compared to healthy controls suggesting that some T cells were able to enter the infected lung tissue, but were not activated and did not include cells with cytotoxic potential (FIG. 1C). In addition, all myeloid, monocyte, and macrophage populations were enriched as well as neutrophils and granulocytes, consistent with a contribution of multiple myeloid cells types contributing to COVID-19 lung pathology (FIG. 1D; FIG. 8B) (Xu et al., 2020).

In the airway, the classical and alternative complement pathways but not the NLRP3 inflammasome signature were enriched in COVID-19 patients as compared to COVID PBMCs (FIG. 1B). We also observed even greater deficiencies in T cells and cytotoxic cells as compared to the peripheral blood (FIG. 1C). Similar to PBMCs from COVID-19 patients, the general myeloid cell gene signature was not enriched in the airway. In contrast, only the M1/M2 macrophage signatures and not the monocyte signature was significantly enriched compared to the blood (FIG. 1D). As a whole, these results highlight the heterogeneity of immune cell types and resulting inflammatory processes in the peripheral blood, lung tissue, and airways of COVID-19 patients.

Increased Expression of Inflammatory Mediators in the Lungs of COVID-19 Patients

To examine the nature of the inflammatory response in the tissue compartments in greater detail, we examined differential expression of specific genes of interest (FIGS. 2A&B). In the blood, we noted increased expression of the inflammatory chemokine CXCL10, which is induced by IFNγ and involved in the activation and chemotaxis of peripheral immune cells (Lindell et al., 2008). We also found increased expression of the chemokine receptor CCR2, which has been shown to be critical for immune cell recruitment in response to respiratory viral infection (FIG. 2A) (Teijaro, 2015). We found few differentially expressed cytokine genes in the blood, but did observe an increase in expression of the inflammatory IL-1 family member, IL18 (FIG. 2B). Expression of a number of chemokines including ligands for CCR2 were significantly increased in both the lung tissue and airway of COVID-19 patients, including CCL2, CCL3L1, CCL7, CCL8, and CXCL10 (FIG. 2A). Whereas the only IL-1 family cytokines significantly enriched in the lung were IL1A and IL1B, we did observe enrichment of the IL-1 cytokine gene signature by GSVA (FIG. 2B; FIG. 8B). In addition to increased expression of chemokine genes shared with the lung tissue (FIG. 2A), many more pro-inflammatory IL-1 family members including IL18, IL33, IL36B, and IL36G were significantly elevated in the airway and not the lung of COVID-19 patients (FIG. 2B).

Non-Hematopoietic Cells in the BAL Fluid May be Indicative of Viral-Induced Damage in the Lungs

To determine whether viral infection in the lungs and airway resulted in modification of resident tissue populations, we evaluated GSVA enrichment of non-hematopoietic cell type gene signatures including fibroblasts, Type I and Type II alveolar cells, ciliated lung cells, club cells, and a general lung tissue cell signature (FIGS. 2C-2E; FIG. 10 ). We found that these non-hematopoietic cell signatures were significantly enriched in the airway, but not the lung. Additionally, we only detected increased expression of the viral entry genes ACE2 and TMPRSS2, which are typically expressed on lung epithelium (ref), in the airway of SARS-CoV2-infected patients (FIG. 2F).

Protein-Protein Interaction Metaclusters Identify Myeloid Cells and Metabolic Pathways in Blood, Lung, and Airway of COVID-19 Patients

We next sought to utilize an unbiased, clustering approach to assess the relationship between immune cell types and the altered biological processes driving SARS-CoV2-mediated pathology within each tissue compartment. Protein-protein interaction (PPI) networks consisting of DE genes were simplified into metastructures defined by the number of genes in each cluster, the number of significant intracluster connections and the number of associations connecting members of different clusters to each other. Overall, upregulated protein networks from blood, lung, and airway of SARS-CoV2-infected patients identified numerous multifunctional clusters many of which included heterogeneous populations of monocyte and myeloid lineage cells. For example, PBMC cluster 8 was dominated by an inflammatory monocyte population defined by C2, C5, CXCL10, CCR2 and multiple interferon-stimulated genes, whereas cluster 3 contained hallmarks of alternatively activated (M2) macrophages and/or myeloid-derived suppressor cells (MDSCs), including CD33, CD36, CD93 and ITGAM (FIG. 3A). Smaller immune clusters were indicative of specific monocyte/myeloid functions, including inflammasome activation (cluster 54), DAMP activity (cluster 17), the classical complement cascade (cluster 34) and the response to Type II interferons (cluster 32). Myeloid heterogeneity was also reflected in the presence of multiple metabolic pathways, such as enhanced oxidative phosphorylation (OXPHOS) in clusters 1 and 4 linked to M2 macrophages, and glycolysis in clusters 7 and 13 used by inflammatory monocytes. Consistent with our GSVA results, peripheral blood exhibited profoundly suppressed T cells determined by the downregulation of T cell activation markers CD28, LCK and ITK (FIG. 11A).

Lung tissue was heavily inflamed exhibiting infiltration of monocyte/myeloid populations with additional infiltration of LDGs, granulocytes, T and B cells. Although distributed among multiple clusters, we observed upregulation of FCN1 (cluster 15), SELL (cluster 14) and S100A8/A9 (cluster 4) which comprise an inflammatory monocyte signature (G1 population) derived from the BAL fluid of COVID patients recently described by Liao et al. (Liao et al., 2020) (FIG. 12A). Metabolic function in the lung was varied, however, upregulated genes segregated with glycolysis, potentially reflecting cellular activation (cluster 18), whereas OXPHOS was predominantly downregulated along with other nuclear processes (transcription and mRNA processing) (FIG. 3B; FIG. 11B).

Finally, the airway was enriched in inflammatory monocytes, mitochondrial function and transcription. Multifunctional cluster 4 was dominated by immune-secreted molecules including numerous chemokine and cytokine receptor-ligand pairs indicative of elevated chemotactic activity, while smaller immune clusters were enriched in classical complement activation (cluster 34), type II interferon (cluster 26) and IL-1 responses (cluster 51). We also observed evidence of recently described alveolar macrophages (AMs; G4 population) specifically in the airway (Liao et al., 2020), although these markers were distributed among multiple clusters, including FABP4 and PPARG in cluster 17, SPP1 and MRC1 in cluster 10, and MARCO and TFRC in clusters 34 and 7, respectively (FIG. 3C, FIG. 12E). The airway was the only compartment with a prominent apoptosis signature located in cluster 47. Consistent with high levels of tissue damage originating from the lung, we observed numerous small clusters reflecting epithelial disruption and non-hematopoietic cell involvement, including clusters 5 and 13 containing multiple intermediate filament keratin genes and cell-cell adhesion claudin genes, respectively. Furthermore, non-hematopoietic cell signatures in the BAL were similar in content to those derived from in vitro COVID19-infected lung epithelium primary cell lines (NHBE) REF (FIG. 11D). Compromised lung function and deep tissue damage was also evident in clusters containing numerous surfactant genes (cluster 43), and the presence of several endothelial (VEGF, PDGFC and DLC1) and fibroblast (ASPN) markers. Similar to the PBMC compartment, T cells were decreased in the airway (FIGS. 11A and 11C).

Myeloid Cell-Derived Metaclusters Define Functional Myeloid Subpopulations within the Blood, Lung, and Airway of Covid-19 Patients

Given the large number of monocyte and myeloid enriched clusters, we next wanted to examine those clusters in greater detail to identify unique myeloid lineage and/or monocyte populations within each tissue compartment. In PBMCs, metaclusters derived from monocyte-enriched clusters revealed new gene modules that were representative of common macrophage function (chemotaxis, proteolysis, etc) as well as two independent monocyte/myeloid subpopulations (FIG. 3D). Cluster 6 contained numerous markers highly reminiscent of classically activated blood monocytes, including C1QA, C1QB, MARCO, TLR4, IRAK1 and was connected to inflammasome genes in cluster 13. Furthermore, clusters 6 and 13 exhibited significant overlap with the inflammatory G1 population defined by Liao et al (2020). In contrast, genes in cluster 1 suggest a second myeloid population characterized by expression of CD33, ITGAM, apoptotic cell clearance (CD93 and MERTK) and high proteolytic capacity. Interestingly, comparison of this population with additional previously defined myeloid populations demonstrated significant overlap with IFN-activated macrophages, CX3CR1+ lining macrophages (arthritis model) and an alveolar macrophage phenotype (FIG. 12F).

Similar to the blood, lung-derived monocyte/myeloid genes segregated into clusters associated with common myeloid-lineage cell functions, such as chemotaxis and pattern recognition, as well as multiple subpopulations (FIG. 3E). Cluster 3 interacted strongly with cluster 6 (interaction score 0.7), containing numerous C-type lectin domain family members involved in cell adhesion, chemotactic receptors (CD74), ligands (CCL8), and FCN1, a recently described marker for highly inflammatory monocytes (G1 population) (Liao et al., 2020). Cluster 6 strongly interacted with pro-migration/chemotaxis cluster 2, and together these clusters exhibited significant overlap with the Liao-defined G1 population, confirming the presence of an infiltrating inflammatory monocyte population in this compartment (FIG. 12F).

Examination of genes in cluster 4 and 7 reveals a potential second myeloid population characteristic of alveolar macrophages (AMs) defined by CSF2RB, which functions as the receptor for GM-CSF, a cytokine that regulates AM differentiation (Joshi et al., 2006; Newton et al., 2016; Suzuki et al., 2014). Interestingly, further characterization of this population indicates significant involvement of the coagulation system indicated by F5, FGG, FGL1, FGL1, SERPINA and SERPINE2.

BAL fluid was also potentially defined by 2 populations, including cluster 7 which had hallmarks of inflammatory/M1 monocytes (MARCO and multiple members of the complement cascade), and AMs in clusters 3 and 5 (FIG. 12F). Cluster 5 was highly enriched in genes related to transcription, but also contained numerous markers for AMs, including APOC1, FABP4 and PPARG and demonstrated significant overlap with the Liao G3 and G4 populations defining “pro-fibrotic” and “lung alveolar macrophages,” respectively (FIG. 12F) (Liao et al., 2020).

Co-Expression Further Delineates Differing Myeloid Gene Expression Between Subpopulations within the Blood, Lung, and Airway of COVID-19 Patients

Both GSVA and PPI networks elucidated the presence of increased myeloid cell populations in all SARS-CoV-2 affected tissues, and PPIs revealed the presence of tissue-specific subpopulations, defined by differing biologic functions. The overlap between many Liao et al. signature genes and the tissue-defined PPI clusters motivated us to further evaluate their enrichment in all tissue compartments. Consistent with PPI clusters, the inflammatory-monocyte like population (G1) was found to be increased in both PBMC and lung, but was significantly decreased in the BAL (FIG. 12A). The G1 and G2 population genes, characterized by predominately interferon-stimulated genes, were increased in the lung (FIG. 12B). Conversely, the “novel intermediate macrophage” population (G2) characterized by inflammatory mediators and chemokines such as CCL2, CCL3 and CCL4, was increased in the BAL, but not the PBMCs (FIG. 12C). Additionally, per patient analyses confirmed the presence of the “pro-fibrotic, SPP1+” macrophage (G3) and “lung alveolar macrophage” populations (G4) in the BAL, although there also may be some evidence of these populations in the lung (FIGS. 12D-12E).

Taken together, evaluation of PPIs and previously published COVID myeloid populations revealed nuances in the myeloid cell populations found among the tissue compartments. We wished to further classify these populations by their expression of traditional myeloid-specific genes including cell surface markers and chemokines. DE interrogation of all possible myeloid cell-specific genes demonstrated further heterogeneity in expression of markers, such as CD14, CD300C, and OSCAR between compartments (FIG. 13 ). GSVA evaluation of both monocyte cell surface and monocyte secreted gene expression confirmed heterogeneous cell surface markers in the BAL, and increased chemokine secretion in the lung (FIG. 4A). To expand upon the PPI framework, and evaluate how these myeloid-specific genes were expressed in relation to our discovered subpopulations, we utilized co-expression analysis. As such, we evaluated the co-expression of 195 monocyte and myeloid cell genes independently in each tissue compartment. For each gene, a Pearson correlation coefficient was calculated with every other myeloid cell gene for both the samples and controls in each tissue compartment (FIG. 14 ). The resultant correlation coefficient matrices were then hierarchically clustered into two clusters based upon co-expression (FIG. 14 ). Each cluster was evaluated in its respective tissue sample and control by GSVA (FIG. 4B). For each compartment, there was a population of genes that were highly co-expressed and altogether increased in each tissue (FIG. 4B). Comparison of the co-expressed genes between each tissue myeloid population shows that many of the increased genes in each tissue are shared (FIG. 4C). The majority of complement genes, including C1QA, C1QB, C1QC C2, C4BPA, and C6 were in included in the 40 genes co-expressed in the increased populations in each compartment. The common co-expressed genes in all tissues also included CCL2, CCL7, CCL8, CXCL10, CCL18, CXCL11, IL18, and TNF. Notably, some of the co-expressed genes unique to the increased COVID lung and BAL populations included CHI3L1, CXCL8, CXCR2, and IL1B, which may be reminiscent of alveolar macrophages. Conversely, these genes were uniquely decreased in the COVID PBMCs.

To characterize the function and nature of these myeloid populations, we again compared them with previously published myeloid signatures including those identified as alveolar macrophages (Reyfman et al., 2019), M1 and M2 populations (Martinez et al., 2006) (Adam's RnD source), and other signatures observed in murine models of inflammatory arthritis (Culemann et al., 2019). Furthermore, we evaluated the overlap between co-expression derived myeloid clusters and those identified using STRING/MCODE PPI in FIG. 3 , as well as macrophages clusters recently evaluated in another cohort of COVID BAL fluid (Liao et al., 2020). We observed significant overlap, as determined by Fisher's Exact Test, in many populations (FIG. 4D).

Of the co-expression derived myeloid clusters increased in each tissue compartment, we observed a progression of classically activated, proinflammatory monocytes from the blood into the lung tissue and in some cases getting sloughed off into the airway, as observed by significant overlap with the PBMC myeloid cluster 6, Lung myeloid clusters 3 and 6, Liao et al.'s proinflammatory population (G1), and the CCR2+IL1B+ infiltrating population (FIG. 4D). Interestingly, we observed a similar trend with the CD33+ MDSC-like pathogenic population (PBMC Myeloid Cluster 1), although the overlap was not as significant as the classically activated, proinflammatory monocyte populations. Contrary to these patterns, we did also observe an M1 macrophage population in all three compartments that was most significantly enriched in the COVID BAL fluid (RnD M1). Upon further investigation into the specific overlapping M1 genes, this observed enrichment was primarily due to the presence of chemokines, proinflammatory cytokines, and activation marker CD80. Additionally, we identified alveolar macrophages in all compartments but primarily in the lung, characterized by inhibitory M2-like gene transcripts, alarmins, chemokines, Fc fragments of the IgG receptor, and CD11c. Despite identification of myeloid populations with features of multiple previously described subtypes, the increased myeloid co-expression derived populations were predominantly proinflammatory and were characterized by pathogenic, activated phenotypes.

Linear Regression Confirms Functional Associations with Myeloid Subpopulations

To confirm the function of these myeloid populations in the pathology of SARS-CoV-2, we performed linear regression analyses between myeloid GSVA scores and functional or signaling pathways. Earlier DE functional enrichment and MCODE/STRING analyses suggested a predominant role for metabolism, particularly glycolysis and the TCA cycle, in PBMCs, as well as OXPHOS in all three tissue compartments. We therefore evaluated metabolism in each compartment using GSVA (FIG. 15 ). We found that the TCA cycle was significantly increased in PBMCs, whereas OXPHOS is significantly increased in the BAL (FIGS. 15C-15D). Additionally, pro-cell cycle genes were increased in PBMCs and pro-apoptosis genes were decreased. We thus evaluated apoptosis and cell cycle on an individual patient basis in each of the compartments using GSVA (FIG. 16 ). Furthermore, both TNF signaling and complement proteins have been noted as relevant to COVID pathology, and these were evaluated by GSVA as well (FIG. 1 ).

Linear regression analyses between GSVA scores for the myeloid cell populations and metabolic, functional, and signaling pathways in each compartment further demonstrated differences among the myeloid cell populations. The myeloid cell population in the PBMCs was found to be highly glycolytic, whereas there was no significant change to metabolism detected in the lung, and the population in the BAL was reliant on OXPHOS (FIG. 5A). Although myeloid cell signatures were associated with the NLRP3 inflammasome in the PBMCs and lungs, this association was not found in the BAL (FIG. 5B). The classical complement cascade was significantly correlated with the increased myeloid cells in both PBMCs and BAL, whereas the alternative complement cascade was significantly correlated with the myeloid cells in the lung (FIG. 5C). The myeloid cells in the PBMCs were also significantly correlated with the cell cycle, but this may be more evident of plasma cells in the blood (FIG. 5D). Additionally, the lung and BAL myeloid populations were negatively correlated with apoptosis (FIG. 5E). As a whole, our analyses reveal the heterogeneity of myeloid cell populations in the blood, lung, and airway of COVID-19 patients in their metabolic and overall inflammatory status, which has critical implications for the role (s) these populations play in COVID-19 pathogenesis.

IPA Confirms Metabolic Activity and Viral, Innate Immunity as Targetable Pathways in COVID-19 Patients

To further inform the biology of SARS-CoV-2-infected patients, we conducted pathway analysis on DEGs from each of the peripheral blood, lung, and airway compartments using IPA canonical signaling pathway and upstream regulator analysis functions (FIG. 6 ). Gene expression fold changes were used to inform statistical overlap with known signaling pathways and molecules upstream of DEGs in SARS-CoV-2. In general, interferon signaling, the inflammasome, and other components of antiviral, innate immunity were reflected by the disease state gene expression profile compared to healthy controls (FIG. 6A). In addition, metabolic pathways including oxidative phosphorylation and glycolysis were significantly activated in SARS-CoV-2 PBMCS compared to controls. Though no differences were found between the PBMCs and BALF in these particular pathways, interestingly, xenobiotic metabolism was predicted to be significantly more activated in the airway indicating a cellular defense response.

Upstream regulators predicted to mediate responses to the virus in each compartment indicated uniform involvement of proinflammatory cytokines with type I interferon regulation dominant in the diseased lung (FIG. 6B). Notable upstream regulators of SARS-CoV-2 peripheral blood included IFNA, IFNG, multiple growth factors and ligands, HIF1A, CSF1 and CSF2; however, when compared to the BALF, upstream regulators of the peripheral blood were more indicative of the presence of lymphocytes. Evidence of proinflammatory cytokine signaling by IL17 and IL36A were predicted in COVID-19 lung and airway compartments. Whereas the BALF DEG profile indicated upstream regulation by both inflammatory and inhibitory cytokines, including IL6 and IL13 and IL10, respectively, the COVID-19 lung upstream regulators were markedly proinflammatory, including, NFκB, IL12, TNF, IL1B, and multiple type I interferons. Small molecules, drugs, and compounds that were predicted as upstream regulators or matched to targets indicate unique therapeutic possibilities in each tissue compartment. Of note, anti-IL17, anti-IL6, anti-IL1, anti-IFNA, anti-IFNG, and anti-TNF treatments were predicted as antagonists of SARS-CoV-2 biology. Steroids were predicted to revert the gene expression profile in the diseased lung, but were predicted as upstream regulators of COVID-19 PBMCs. Finally, chloroquine was additionally predicted to revert the SARS-CoV-2 transcription profile in the lung.

Discussion

In the present study, we utilize multiple orthogonal bioinformatics approaches to analyze differential gene expression from the blood, lung, and airway of COVID-19 patients. As a whole, our results are in agreement with the current understanding of SARS-CoV2 pathogenesis, which generally involves lymphopenia accompanied by increased activation of pro-inflammatory pathways and myeloid cells (Tay et al.). In particular, we found that DE genes from COVID-19 patients were enriched in gene signatures of interferon, complement pathways, and the inflammasome, which would be expected to initiate a robust and systemic response to infection. We also utilized various approaches to derive and characterize the expanded myeloid cell subpopulations in COVID-19 patients. These observed increases in inflammatory pathways and myeloid cell subsets are likely reflective of a dysregulated immune response that contributes to lung damage, and in severe cases, to multi-organ failure and overall poor health outcomes in COVID-19 patients. Furthermore, by comparing DE results from multiple compartments (the blood, lung, and airway) in COVID-19 patients, we have developed a model of the systemic pathogenic response to SARS-CoV2 infection (FIG. 7 ).

In our proposed model, after viral exposure, SARS-CoV2 enters the host airway and infects alveolar epithelial cells, which express the virus entry receptors ACE2 and TMPRSS2. In the lung tissue, we observed increased expression of Type I interferon genes, enrichment of Type I and Type II interferon gene signatures, and expression of IFN-stimulated genes including TNF and NOS2. Type I interferons are critical components of the host response to viral infection through inducing the expression of anti-viral genes and direct or indirect immune cell activation and, thus, are targets of immune evasion tactics by coronaviruses including SARS-CoV and MERS-CoV (Newton et al., 2016; Tay et al.). Type I interferons can be produced by virus-infected cells, or cells that have detected viral infection (Goritzka et al., 2015). Therefore, interferon production in the lung of COVID-19 patients is likely initiated by infected alveolar cells and propagated by activated alveolar macrophages, leading to the production of IFNγ and other pro-inflammatory mediators (Darwich et al., 2009; Newton et al., 2016). To date, reports have been divided over whether an interferon response is present in COVID-19 patients in that some reports cite a poor interferon response (Blanco-Melo et al., 2020), some observe a robust interferon response that increases with disease severity (Wei et al., 2020), and still others have found heterogeneity in whether patients exhibit an interferon response to SARS-CoV2 infection (Trouillet-Assant et al., 2020). Therefore, the interferon response to SARS-CoV2 requires further study and consideration when developing treatment strategies for individual patients.

Signals from the lung including interferon or other pro-inflammatory mediators from infected cells disseminate into the peripheral blood to launch a systemic inflammatory response. In the periphery, inflammatory mediators from the lung typically promote activation and migration of myeloid cells, NK cells, and adaptive immune cells including T and B cells, which can differentiate into effector CD8 T cells and antibody-producing plasma cells (Newton et al., 2016). We found significant deficiencies in gene signatures of T cells, NK cells, and cytotoxic cells, which include activated CD8 T cells and NK cells, in the peripheral blood of COVID-19 patients, which is consistent with clinical and analytical evidence of lymphopenia following SARS-CoV and SARS-CoV2 infection (Chen et al., 2020b; He et al., 2005; Qin et al., 2020; Xu et al., 2020). In contrast to T and NK cells, we observed increased evidence of B cell activation through CD40/CD40L and an increased plasma cell signature in PBMCs of COVID-19 patients. This result suggests that while effector CD8 T cells are deficient, that helper T (Th) cells are present and able to promote B cell activation, the generation of antibody secreting plasma cells, and an antibody-mediated immune response. However, whether a virus-specific antibody response is beneficial to recovery from SARS-CoV2 infection is unclear (Wu et al., 2020). Evidence from SARS-CoV infection suggests that the quality of the antibody produced is critical to mounting an effective anti-viral response. Low quality, low affinity antibody responses may have pathological consequences including promoting lung injury in some patients, although it is unknown if this occurs in SARS-CoV2 infected individuals (Iwasaki and Yang, 2020; Liu et al., 2019).

The predominant populations of immune cells we found to be enriched and activated in COVID-19 patients were myeloid cells and, in particular, subsets of inflammatory monocytes and macrophages, which differed between the blood, lung, and airway compartments. In the peripheral blood, we found significant enrichment of monocytes including classically activated inflammatory monocytes as well as another subset characterized by expression of CD33. This CD33⁺ myeloid subset appeared to be an alternatively activated population reminiscent of previously characterized IFN-activated macrophages and alveolar macrophages (AMs), which may represent an activation state specific to stimuli arising from the SARS-CoV2-infected lung. Myeloid cells enriched in the blood of COVID-19 patients were also correlated with pro-cell cycle and glycolysis gene signatures indicative of a metabolic status associated with pro-inflammatory M1 macrophages (Viola et al., 2019). In support of the presence of increased pro-inflammatory monocytes/macrophages, we also found significant increases in the expression of the pro-inflammatory IL-1 family member IL18, the interferon-induced chemokine CXCL10, and the chemokine receptor CCR2, all of which have cited roles in the response to respiratory virus infection (Tang et al., 2005; Teijaro, 2015; Wang et al., 2004).

In the lung tissue, we observed increased expression of a number of chemokine ligands for CCR2 (CCL2, CCL7, CCL8) and other receptors (CCL3, CXCL10, CXCL16), which would promote the mobilization of activated immune cells to the locus of infection. While in the blood, we found evidence of increased monocyte/macrophage populations, in the lung tissue, we also observed enrichment of gene signatures of other myeloid cells including neutrophils and low density granulocytes (LDGs), which we could not assess in the blood due to the process of isolating PBMCs. The role of neutrophils and LDGs in COVID-19 pathogenesis has been poorly characterized although they have been found in increased numbers and associated with poor disease outcome in COVID-19 patients (Huang et al., 2020). In addition, some have proposed that the formation of neutrophil extracellular traps (NETs) contributes to increased multi-organ damage and risk of death from SARS-CoV2 infection (Barnes et al., 2020; Thierry and Roch, 2020).

Monocyte/macrophage subsets in the lung of COVID-19 patients were characterized as infiltrating inflammatory monocytes and activated AMs, which exhibited a mixed metabolic status suggestive of different states of activation. Infiltrating monocytes from the peripheral blood appeared to be further activated in the lung tissue as evidenced by enhanced expression of alarmins and markers of highly inflammatory monocytes previously characterized in severe COVID-19 cases (Liao et al., 2020). In particular, we observed increased expression of IL-1 family members, most notably ILIA and enrichment of a pro-inflammatory IL-1 signature in the lung of COVID-19 patients. We also found evidence of a population of AMs previously defined in the BAL of COVID-19 patients (Liao et al., 2020). Alveolar macrophages are typically suppressed at steady state, but adopt a pro-inflammatory phenotype after viral infection in order to assist in phagocytosis and clearance of virus (Newton et al., 2016). However, we observed that this AM population also clustered with genes involved in the coagulation system, which is consistent with observations of procoagulant AM activity in ARDs (Tipping et al., 1988). As pulmonary thrombosis has been associated with poor clinical outcomes in COVID-19 patients, this result suggests that AMs in SARS-CoV2-infected lung tissue may be detrimental to host recovery from disease (Wichmann et al., 2020).

While we observed significant decreases in T cells in the blood of COVID-19 patients, they appeared to be increased in the lung tissue. However, upon closer examination, we noted that there was no enrichment of activated T cells or of cytotoxic CD8 T cells. This indicated that while T cells may be able to enter the infected lung tissue, they are not activated and thus lack the ability to clear virus-infected cells and resolve the inflammatory response. In cases of macrophage activation syndrome (MAS) defects in cytotoxic activity of CD8 T cells and NK cells result in increased cell-cell contacts, enhanced immune cell activation, and intensified production of pro-inflammatory cytokines. Many of the pro-inflammatory cytokines associated with MAS were also expressed in our COVID-19 patient samples, predominantly in the lung tissue and airway compartments, including IL1, IL18, and IL33 (Crayne et al., 2019; McGonagle et al., 2020). Thus, it is likely that the lack of activated CD8 T cells and NK cells and subsequent failure to clear virus-infected cells, is a major contributor to the dysregulated, macrophage-driven pathologic response to SARS-CoV2 observed in COVID-19 patients.

As disease progresses, increased infiltration of pro-inflammatory immune cells and release of inflammatory mediators in the lung is emulated by the presence of immune cells in the airway, which can be sampled through the BAL (Heron et al., 2012). Thus, the contents of the BAL fluid acts as a diagnostic marker or sensor for what is occurring in the lung tissue. In the airway, we detected gene signatures of various post-activated macrophage subsets including inflammatory M1 macrophages, alternatively activated M2 macrophages, and activated alveolar macrophages that had either migrated or been shed from the lung tissue. In conjunction with the presence of inflammatory macrophages, our results revealed a prominent IL-1 family signature in the airway of COVID-19 patients above what we observed in the blood or lung tissue and, in particular, an over 10-fold increase in expression of the alarmins ILIA and IL33 (Jing et al., 2016; Schmitz et al., 2005). These alarmins act as danger signals released by dead or dying cells to promote immune cell activation and therefore, their presence in the airway is likely indicative of an increase in virally infected lung cells. As SARS-CoV2 continues to propagate and viral clearance is impaired by a lack of cytotoxic activity, these alarmins promote inflammation and prevent resolution of the immune response in COVID-19 patients. Thus, this result further supports the notion that IL-1-mediated inflammation plays a critical role in COVID-19 pathogenesis. Expression of myeloid cell genes in the airway also correlated with a signature of oxidative metabolism, which is characteristic of M2 macrophages and typically associated with control of tissue damage (Viola et al., 2019). However, in the context of pulmonary infection, polarization of alveolar macrophages toward an anti-inflammatory M2 phenotype was found to promote continued pathogenesis, suggesting that these macrophages may not be effective mediators of anti-viral immunity (Allard et al., 2018).

We found increased enrichment of lung epithelial cells as well as increased expression of the viral entry receptors ACE2 and TMPRSS2, which are expressed by these cells, exclusively in the airway of COVID-19 patients. The presence of non-hematopoietic cells such as lung epithelium in the BAL is indicative of damage to the lung tissue as dead or dying cells are being sloughed off into the airway and suggests that localized inflammation as a result of enhanced immune cell infiltration promotes significant damage to the lung tissue. Furthermore, the lack of cytotoxic cells and thus, the inability to clear these virus-infected lung epithelial cells in the airway likely accounts for the increased presence of post-activated macrophages and high expression of pro-inflammatory IL-1 family members we observed in the BAL of COVID-19 patients. However, in contrast to previous characterizations of both SARS-CoV and SARS-CoV2 infection, our analysis did not indicate the presence of overwhelming pro-inflammatory cytokine production or “cytokine storm” (Tay et al.). Rather our data suggests that the increased numbers, overactivation, and potentially heightened pathogenicity of monocyte/macrophage populations are the main drivers of the dysregulated immune response and resulting tissue damage in COVID-19 patients.

Big Data Analyses Facilitate Drug Prediction

In the absence of effective antiviral treatment and/or a SARS-CoV2-specific vaccine, disease management is reliant upon supportive care and therapeutics capable of limiting the severity of clinical manifestations. Using empirical evidence as a guide, the current approach has been successful in identifying “actionable” points of intervention in an unbiased manner and in spite of formidable patient heterogeneity. Analyses presented here support several recent reports highlighting COVID19 infection-related increases in secreted factors, particularly IL6 and TNF, both of which function as predictors of poor prognosis (Pedersen and Ho, 2020; Voiriot et al., 2017), as well as complement activation (Gao et al., 2020; Huang et al., 2020; Mehta et al., 2020). Accordingly, anti-IL6 therapies including sarilumab, tocilizumab and clazakizumab, as well as biologics targeting terminal components of the complement cascade, such as eculizumab and ravulizumab, are in various clinical trial phases for treating COVID19 associated pneumonia. Candidate TNF blockers such as adalimumab, entanercept and many others, represent additional options for inhibiting deleterious pro-inflammatory signaling. Interestingly, numerous tubulin inhibitors were identified among the complied list of drugs counteracting infection-induced genomic changes; it is therefore of note that clinical trials involving colchicine, an antimitotic drug that binds soluble tubulin, are currently underway, providing further validation for the unbiased drug-prediction methodology presented here. Our analyses also point to the likely involvement of pro-inflammatory IL1 family members especially in the lung, suggesting anti-IL1 interventions, including canakinumab and anakinra, may be effective in preventing acute lung injury.

Overall, this report establishes the predominance of inflammatory monocyte/myeloid lineage cells in driving disease pathology and suggest therapies effective at blocking myeloid cell recruitment or forcing repolarization may prevent disease progression. CCL5 (RANTES) is a potent leukocyte chemoattractant that interacts with multiple receptors, including CCR1 (upregulated in the blood, lung and airway), and CCR5 (upregulated in the airway). Disruption of the CCR5-CCL5 axis was recently tested using the CCR5 blocking monoclonal antibody leronlimab in a small compassionate use trial with promising preliminary results (Pattterson et al.). Similarly, CD74 which functions as the receptor for the pro-inflammatory cytokine macrophage migration inhibitory factor (MIF), was upregulated specifically in the lung and represents an attractive target for intervention by imalumab, an anti-MIF monoclonal antibody.

It has also been observed that COVID19 may predispose patients to thromboembolic disease (Klok et al., 2020; Middeldorp et al., 2020). Indeed, the gene expression analyses presented here showing altered expression of coagulation factors and fibrinogen genes suggests dysfunction within the intrinsic clotting pathway. These findings, together with evidence of excessive inflammation and complement activation, may contribute to the systemic coagulation underlying the remarkably high incidence of thrombotic complications observed in severely ill patients, thereby reinforcing recommendations to apply pharmacological anti-thrombotic medications.

Finally, there has been much recent discussion concerning the use of anti-rheumatic drugs for managing COVID19. In fact, chloroquine (CQ) was one compound predicted as an upstream regulator with potential phenotype-reversing properties. In vitro experiments examining the anti-viral properties of CQ and its derivative hydroxychloroquine (HCQ) were effective in limiting viral load, however the efficacy of these drugs in clinical trials has been less clear. Questions about drug timing, dosage and adverse events have all called into question the use of these drugs for COVID19 patients.

Using systems and methods of the present disclosure, a treatment may be selected for an individual based on data analyses of biological samples obtained from the individual, in order to treat or manage a COVID19 disease state or condition of the individual. For example, a targeted treatment for the blood may be selected for an individual based on data analyses of biological samples obtained from the individual, in order to treat or manage a COVID19 disease state or condition of the individual. For example, a targeted treatment for the lungs may be selected for an individual based on data analyses of biological samples obtained from the individual, in order to treat or manage a COVID19 disease state or condition of the individual. For example, a targeted treatment for the airways may be selected for an individual based on data analyses of biological samples obtained from the individual, in order to treat or manage a COVID19 disease state or condition of the individual. In some embodiments, the treatment may be selected from among a plurality of different treatments for an individual based on data analyses of biological samples obtained from the individual, in order to treat or manage a COVID19 disease state or condition of the individual.

Weighted Gene Co-Expression Network Association

DEseq2 normalized log 2 transformed RNAseq gene counts for CRA2390 and GSE147507 datasets were used as inputs to WGCNA (V1.69). Adjacency co-expression matrices for all genes in a given set were calculated by Pearson's correlation using signed network type specific formulae. Blockwise network construction was performed using a soft threshold power value of 30 in order to preserve maximal scale free topology of the networks. Resultant dendrograms of correlation networks were trimmed to isolate individual modular groups of genes, labeled using semi-random color assignments, based on a detection cut height of 1, with a merging cut height of 0.2, with the additional use of a partitioning around medoids function. The module eigenegene (ME) vector per sample was calculated as the first principle component of the module's gene expression counts. Module correlations to cohort were calculated using Pearson's r against MEs, defining modules as either positively or negatively correlated as a whole by averaging constituent sample ME correlations to cohort. The strength of module representation was established by inspecting the number of members of the disease or healthy samples contributing to the overall average ME correlation to disease state. Majority modules highly representative of their cohort were those where more than half of the cohort constituent MEs were correlated in the same direction and general scale to cohort. Quality majority modules were those with the additional requirement that the opposing cohort correlations were all running in the opposite direction. Minority quality disease state modules were considered as being more representative of genetic expressions unique to patient rather than cohort. Module membership statistics were calculated including kIM, a measurement of intramodular connectivity of each gene's expression values across samples to neighboring module genes, kME, the correlation of each gene to its containing module eigengene, and general correlation of gene expression values to cohort. Hub genes were considered as those with the highest kIMs, and as a general rule also had the highest kMEs. Complete composite module preservation statistics were calculated using WGCNA's modulePreservation function through 200 permutations of the three data sets independently tested against each other as either a reference or test set. The Z summary statistic was selected as the global index of module preservation and is a composite of seven density and connectivity preservation statistics. All constituent statistics were retained for future granular analysis. Modules were considered as moderately preserved between reference-test network pairs as those with a Z summary statistic between 5 and 10, and as highly preserved as those with a Z summary score above 10. Preservation median rank was calculated to scale module preservation to module size. Gene symbols common between moderately and highly preserved modules in each reference-test pair were selected for ensuing GSVA enrichment analysis.

MEGENA Gene Co-Expression Network Association

The MEGENA (Multiscale Embedded Gene Co-expression Network Analysis) package (v1.3.7) was applied to reconstruct co-expression networks, as described by, for example, [Won-Min Song and Bin Zhang (2018). MEGENA: Multiscale Clustering of Geometrical Network. R package version 1.3.7. CRAN.R-project.org/package=MEGENA], which is incorporated by reference herein in its entirety. The DEseq2 normalized log 2 transformed RNAseq gene counts used for WGCNA analysis were used for initial MEGENA correlation calculation. Gene expression rows with a standard deviation of less than 0.2 were discarded. The correlations between all remaining gene pairs was calculated using Pearson's correlation coefficient (φ using MEGENA's calculation correlation function. After calculation of true pairwise ρ values, a permutation procedure determined the necessary ρ value necessary to achieve a false positive rate (FPR) of 0.05. The gene expression matrix was shuffled through 10 permutations and ρ coefficient results were pooled. Gene correlations greater than an FPR of 0.05 were discarded. An FDR threshold of 15% was additionally enforced to reduce type-one errors. Thresholded FDR correlations were submitted to the MEGENA package for generation of a planar filtered network (PFN) of genes mapped to each other through network connectivity strength. Briefly, gene pairs were first ranked based on expression similarity and then iteratively tested for planarity to expand the PFN, while favoring those pairs with larger similarities. Multi-scale module structures were generated through Multiscale Clustering Analysis (MCA) by clustering initial connected components of the PFN as parent clusters, with clustering repeated in an iterative fashion down through module lineages until no meaningful descendent modules remained to split. A minimum module size of 20 genes was enforced throughout. Multiscale Hub Analysis (MHA) was performed to detect significant hubs of individual clusters and across a, characterizing different scales of organizations in the PFN with emphasis given to multiscale hubs. Significant MEGENA modules were selected that showed a significance of compactness by p<0.05. Analogous to WGCNA, Cluster-Trait Association Analysis (CTA) was performed by performing principle component analysis (PCA) on each module and correlated to cohort, with correlation significance set to Fisher's adjust p value <0.05. First-generation modules (founding members of their lineage) were examined for various cell and pathway signature gene set variation analysis (GSVA) enrichments, with significant enrichments as those with a Hedge's corrected adjusted p value <0.05. MEGENA modules were coerced into WGCNA's module preservation function and analyzed as before by considering overlapping genes from reference-test network pairs with a mutual minimum composite Z summary statistic of 5. MEGENA modules were renamed to indicate their pedigree and networks were visualized using sunburst diagrams to depict module lineages. Some sunbursts were colored using majority WGCNA color assignment to elucidate differences in module creation between the MEGENA and WGCNA approaches. Some were colored using majority cell signature enrichment to demonstrate inheritance of cell signature through module lineage, and others colored with gene expression log-fold change. Heatmaps of log 2 transformed module gene expression were inspected to establish how well modules represented their cohort, similar to majority and minority quality WGCNA modules. Heatmaps were also generated of various module GSVA cell signature enrichments to further curate modules of immunological and other interests.

Module Gene Co-Expression Network Visualization

Modules showing high enrichment of cell signatures of interest were selected for additional enrichment analysis, pathway annotation, and network visualization. Module official HGNC gene symbols were imported into Cytoscape (v3.8.0) through its STRING (v11) protein query set to a confidence score cutoff of 0.9 with zero allowed maximum additional interactions. Cytoscope is described by, for example, [Shannon P, Markiel A, Ozier O, Baliga N S, Wang J T, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res, 13:11 (2498-504). 2003 November PubMed ID: 14597658], which is incorporated by reference herein in its entirety. String is described by, for example, [Szklarczyk D, Gable A L, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva N T, Morris J H, Bork P, Jensen L J, von Mering C. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019 January; 47:D607-613], which is incorporated by reference herein in its entirety. Edges (connections) between gene nodes were weighted as the STRING connection strengths. Genes with less than 3 connections to adjacent nodes were discarded. MCODE clustering was calculated on the whole network with a degree cutoff of 2 and clusters found allowing haircut and fluff, and some visualizations colored by MCODE cluster, as described by, for example, [Bader G D, Hogue C W. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics, 4: (2). 2003 Jan. 13. PubMed ID: 12525261], which is incorporated by reference herein in its entirety. AMPEL cell signature annotations were merged to the nodes data table and used to adjust node color, border color, and sizes to call out genes of interest. Various attribute and network cluster algorithms from the Cytoscape clusterMaker app were applied to help simplify visualizations, including GLay community clustering, as described by, for example, [Morris J H, Apeltsin L, Newman A M, Baumbach J, Wittkop T, Su G, Bader G D, Ferrin T E. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics, 12: (436). 2011 Nov. 9. PubMed ID: 22070249], which is incorporated by reference herein in its entirety. BiNGO was used to query various GO (gene ontology) pathways to further elucidate network relations to biological processes, as described by, for example, [Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21:16 (3448-9). 2005 Aug. 15. PubMed ID: 15972284], which is incorporated by reference herein in its entirety. Clusters from various modules were visualized together and examined for interconnectedness. Meta clusters were created by combining genes with similar functional annotation into composite nodes, with edges between them weighted as the total number of MCODE connections between constituent genes.

Derivation of Lung Tissue Cell Populations for GSVA

Nine single-cell RNA-seq lung cell populations (AT1, AT2, Ciliated, Club, Endothelial, Fibroblasts, Immuno Monocytes, Immuno T Cells, and Lymphatic Endothelium) were downloaded from the Eils Lung Tissues set (www.biorxiv.org/content/10.1101/2020.03.13.991455v3) accessed by the UC Santa Cruz Genome Browser (eils-lung.cells.ucsc.edu). Genes occurring in more than one cell type were removed. Additionally, genes known to be expressed by immune cells were removed. The Immuno Monocyte and Immuno T cell categories were not employed in further analyses.

Derivation of Co-Expressed Myeloid Subpopulations in Each Compartment

Co-expression analyses were conducted in R. Sample (control and patient) log 2 expression values for each gene of the 221 identified monocyte/myeloid cell genes in were analyzed for their Pearson correlation coefficient in each tissue compartment (PBMC, lung, BAL) using the Cor function. Of note, only 195 of 221 genes had changes in gene expression in at least one tissue by RNA-seq, and these genes are shown. Resulting correlation matrices were hierarchically clustered by their Euclidian distance into 2 clusters (k=2) using the heatmap.2 function in R. This resulted in 2 monocyte/myeloid co-expressed clusters in each compartment. The co-expressed myeloid populations in each compartment were then evaluated by GSVA.

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Table of 33 Modules geneSymbol geneEntrezID GeneSet CD160 11126 Anergic/Activated T cells CD244 51744 Anergic/Activated T cells CTLA4 1493 Anergic/Activated T cells HAVCR2 84868 Anergic/Activated T cells ICOS 29851 Anergic/Activated T cells KLRG1 10219 Anergic/Activated T cells LAG3 3902 Anergic/Activated T cells PDCD1 5133 Anergic/Activated T cells IL1RN 3557 Anti inflammation TNFAIP3 7128 Anti inflammation SOCS3 9021 Anti inflammation IGHD 3495 B cells SH3BP5 9467 B cells BANK1 55024 B cells BLK 640 B cells BLNK 29760 B cells CD19 930 B cells CD22 933 B cells CD79A 973 B cells CD79B 974 B cells DAPP1 27071 B cells FCRL1 115350 B cells FCRL2 79368 B cells FCRL3 115352 B cells FCRLA 84824 B cells GON4L 54856 B cells GPR183 1880 B cells IGHM 3507 B cells KLHL6 89857 B cells MS4A1 931 B cells PAX5 5079 B cells PLCL2 23228 B cells VPREB1 7441 B cells ZNF318 24149 B cells CD8A 925 CD8T-NK-NKT CD8B 926 CD8T-NK-NKT GZMB 3002 CD8T-NK-NKT NKTR 4820 CD8T-NK-NKT CD2 914 CD8T-NK-NKT CD7 924 CD8T-NK-NKT CRTAM 56253 CD8T-NK-NKT GNLY 10578 CD8T-NK-NKT GZMA 3001 CD8T-NK-NKT GZMK 3003 CD8T-NK-NKT GZMM 3004 CD8T-NK-NKT HCST 10870 CD8T-NK-NKT KIR2DL3 3804 CD8T-NK-NKT KIR3DL1 3811 CD8T-NK-NKT KIR3DL2 3812 CD8T-NK-NKT KLRB1 3820 CD8T-NK-NKT KLRC3 3823 CD8T-NK-NKT KLRC4 8302 CD8T-NK-NKT KLRD1 3824 CD8T-NK-NKT NKG7 4818 CD8T-NK-NKT RASAL3 64926 CD8T-NK-NKT TIA1 7072 CD8T-NK-NKT TXK 7294 CD8T-NK-NKT BRCA1 672 Cell Cycle ASPM 259266 Cell Cycle AURKA 6790 Cell Cycle AURKB 9212 Cell Cycle CCNB1 891 Cell Cycle CCNB2 9133 Cell Cycle CCNE1 898 Cell Cycle CDC20 991 Cell Cycle CENPM 79019 Cell Cycle CEP55 55165 Cell Cycle E2F3 1871 Cell Cycle GINS2 51659 Cell Cycle MCM10 55388 Cell Cycle MCM2 4171 Cell Cycle MKI67 4288 Cell Cycle NCAPG 64151 Cell Cycle NDC80 10403 Cell Cycle PTTG1 9232 Cell Cycle TYMS 7298 Cell Cycle GZMB 3002 Cytotoxic, Activated T cells TAGAP 117289 Cytotoxic, Activated T cells CD69 969 Cytotoxic, Activated T cells EOMES 8320 Cytotoxic, Activated T cells GZMH 2999 Cytotoxic, Activated T cells IFNG 3458 Cytotoxic, Activated T cells IL2RB 3560 Cytotoxic, Activated T cells PRF1 5551 Cytotoxic, Activated T cells SGK1 6446 Cytotoxic, Activated T cells TBX21 30009 Cytotoxic, Activated T cells TFRC 7037 Cytotoxic, Activated T cells ZNF683 257101 Cytotoxic, Activated T cells CLEC12A 160364 Dendritic CLEC10A 10462 Dendritic CLEC9A 283420 Dendritic CSF1R 1436 Dendritic IGIP 492311 Dendritic LILRA4 23547 Dendritic LY75 4065 Dendritic XCR1 2829 Dendritic EPO 2056 Erythrocytes GFI1B 8328 Erythrocytes GYPA 2993 Erythrocytes GYPB 2994 Erythrocytes GYPE 2996 Erythrocytes ICAM4 3386 Erythrocytes NFE2 4778 Erythrocytes SLC4A1 6521 Erythrocytes TRIM10 10107 Erythrocytes TSPO2 222642 Erythrocytes ZNF367 195828 Erythrocytes CXCR2 3579 Granulocyte CD177 57126 Granulocyte CLC 1178 Granulocyte CTSS 1520 Granulocyte DEFA1 1667 Granulocyte FUT7 2529 Granulocyte LTB4R 1241 Granulocyte MMP25 64386 Granulocyte OSM 5008 Granulocyte RETN 56729 Granulocyte GBP1 2633 IFN IFI44 10561 IFN MX1 4599 IFN NAMPT 10135 IFN NKTR 4820 IFN NR3C1 2908 IFN OAS3 4940 IFN PATJ 10207 IFN TAP2 6891 IFN TNFRSF11A 8792 IFN FASLG 356 IFN WT1 7490 IFN EIF2AK2 5610 IFN GBP2 2634 IFN GBP4 115361 IFN HERC5 51191 IFN HERC6 55008 IFN IFI27 3429 IFN IFI30 10437 IFN IFI35 3430 IFN IFI44L 10964 IFN IFI6 2537 IFN IFIT1 3434 IFN IFIT2 3433 IFN IFIT3 3437 IFN IFIT5 24138 IFN IFITM1 8519 IFN IFITM2 10581 IFN IFITM3 10410 IFN ISG15 9636 IFN ISG20 3669 IFN MX2 4600 IFN NFE2L3 9603 IFN NMI 9111 IFN NUB1 51667 IFN NUPR1 26471 IFN OAS1 4938 IFN OAS2 4939 IFN OASL 8638 IFN PDGFB 5155 IFN PDGFRL 5157 IFN PKD2 5311 IFN PLSCR1 5359 IFN PMAIP1 5366 IFN PML 5371 IFN PRKRA 8575 IFN PSMB9 5698 IFN PTCH1 5727 IFN RBCK1 10616 IFN RGS1 5996 IFN RGS6 9628 IFN RSAD2 91543 IFN RTP4 64108 IFN SAMD9 54809 IFN SAMD9L 219285 IFN SAT1 6303 IFN SCARB2 950 IFN SERPING1 710 IFN SIT1 27240 IFN SOCS1 8651 IFN SP100 6672 IFN SP110 3431 IFN SP140 11262 IFN SPIB 6689 IFN ST3GAL5 8869 IFN STAP1 26228 IFN STAT1 6772 IFN STAT2 6773 IFN STX11 8676 IFN SUPT3H 8464 IFN TAP1 6890 IFN TARBP1 6894 IFN TCN2 6948 IFN TFDP2 7029 IFN TGM1 7051 IFN TLR3 7098 IFN TLR7 51284 IFN TNFSF10 8743 IFN TNK2 10188 IFN TOR1B 27348 IFN TRA2B 6434 IFN TRD 6964 IFN TRIM21 6737 IFN TRIM22 10346 IFN TRIM34 53840 IFN TRIM38 10475 IFN UBA7 7318 IFN UBE2L6 9246 IFN UBE2S 27338 IFN UNC93B1 81622 IFN USP18 11274 IFN WARS 7453 IFN XAF1 54739 IFN IGHG1 3500 IG CHAINS IGHV2-5 28457 IG CHAINS IGHV3-20 28445 IG CHAINS IGHV3-23 28442 IG CHAINS IGHV4-28 28400 IG CHAINS IGHV4-34 28395 IG CHAINS IGKC 3514 IG CHAINS IGLV1-40 28825 IG CHAINS IGLV3-1 28809 IG CHAINS IGLV3-19 28797 IG CHAINS IGLV3-25 28793 IG CHAINS IGLV4-3 28786 IG CHAINS IGLV4-60 28785 IG CHAINS IGLV5-45 28781 IG CHAINS IGLV6-57 28778 IG CHAINS IGLVI-70 28763 IG CHAINS IGHA1 3493 IG CHAINS IGHA2 3494 IG CHAINS IGHD2-15 28503 IG CHAINS IGHD2-2 28505 IG CHAINS IGHD2-21 28502 IG CHAINS IGHD3-10 28499 IG CHAINS IGHD3-16 28498 IG CHAINS IGHD3-3 28501 IG CHAINS IGHD3-9 28500 IG CHAINS IGHG2 3501 IG CHAINS IGHG3 3502 IG CHAINS IGHG4 3503 IG CHAINS IGHJ1 28483 IG CHAINS IGHJ2 28481 IG CHAINS IGHJ3 28479 IG CHAINS IGHJ4 28477 IG CHAINS IGHJ5 28476 IG CHAINS IGHJ6 28475 IG CHAINS IGHV1-18 28468 IG CHAINS IGHV1-2 28474 IG CHAINS IGHV1-24 28467 IG CHAINS IGHV1-3 28473 IG CHAINS IGHV1-45 28466 IG CHAINS IGHV1-46 28465 IG CHAINS IGHV1-58 28464 IG CHAINS IGHV1-69-2 28458 IG CHAINS IGHV2-26 28455 IG CHAINS IGHV2-70 28454 IG CHAINS IGHV3-13 28449 IG CHAINS IGHV3-15 28448 IG CHAINS IGHV3-21 28444 IG CHAINS IGHV3-33 28434 IG CHAINS IGHV3-43 28426 IG CHAINS IGHV3-48 28424 IG CHAINS IGHV3-49 28423 IG CHAINS IGHV3-53 28420 IG CHAINS IGHV3-62 28416 IG CHAINS IGHV3-64 28414 IG CHAINS IGHV3-7 28452 IG CHAINS IGHV3-72 28410 IG CHAINS IGHV3-73 28409 IG CHAINS IGHV3-74 28408 IG CHAINS IGHV4-30-2 28398 IG CHAINS IGHV4-39 28394 IG CHAINS IGHV4-59 28392 IG CHAINS IGHV4-61 28391 IG CHAINS IGHV5-51 28388 IG CHAINS IGHV6-1 28385 IG CHAINS IGHV7-81 28378 IG CHAINS IGKJ1 28950 IG CHAINS IGKJ2 28949 IG CHAINS IGKJ3 28948 IG CHAINS IGKJ4 28947 IG CHAINS IGKJ5 28946 IG CHAINS IGKV1-16 28938 IG CHAINS IGKV1-17 28937 IG CHAINS IGKV1-27 28935 IG CHAINS IGKV1-5 28299 IG CHAINS IGKV1-6 28943 IG CHAINS IGKV1-9 28941 IG CHAINS IGKV1D-16 28901 IG CHAINS IGKV1D-17 28900 IG CHAINS IGKV1D-43 28891 IG CHAINS IGKV1D-8 28904 IG CHAINS IGKV2-24 28923 IG CHAINS IGKV2D-26 28884 IG CHAINS IGKV2D-29 28882 IG CHAINS IGKV2D-30 28881 IG CHAINS IGKV3-20 28912 IG CHAINS IGKV3D-20 28874 IG CHAINS IGKV3D-7 28877 IG CHAINS IGKV4-1 28908 IG CHAINS IGKV5-2 28907 IG CHAINS IGLC2 3538 IG CHAINS IGLC7 28834 IG CHAINS IGLJ6 28828 IG CHAINS IGLV10-54 28772 IG CHAINS IGLV1-36 28826 IG CHAINS IGLV1-47 28822 IG CHAINS IGLV2-11 28816 IG CHAINS IGLV2-18 28814 IG CHAINS IGLV2-23 28813 IG CHAINS IGLV2-33 28811 IG CHAINS IGLV2-8 28817 IG CHAINS IGLV3-10 28803 IG CHAINS IGLV3-12 28802 IG CHAINS IGLV3-16 28799 IG CHAINS IGLV3-21 28796 IG CHAINS IGLV3-27 28791 IG CHAINS IGLV3-32 28787 IG CHAINS IGLV4-69 28784 IG CHAINS IGLV5-37 28783 IG CHAINS IGLV7-43 28776 IG CHAINS IGLV8-61 28774 IG CHAINS IGLV9-49 28773 IG CHAINS IL18 3606 IL1 cytokines IL1B 3553 IL1 cytokines CASP1 834 Inflammasome AIM2 9447 Inflammasome CASP5 838 Inflammasome CTSB 1508 Inflammasome GSDMB 55876 Inflammasome GSDMD 79792 Inflammasome NAIP 4671 Inflammasome NEK7 140609 Inflammasome NLRC4 58484 Inflammasome NLRP1 22861 Inflammasome NLRP3 114548 Inflammasome NOD2 64127 Inflammasome P2RX7 5027 Inflammasome PANX1 24145 Inflammasome PYCARD 29108 Inflammasome RIPK1 8737 Inflammasome AZU1 566 LDG CAMP 820 LDG CEACAM6 4680 LDG CEACAM8 1088 LDG CTSG 1511 LDG DEFA4 1669 LDG ELANE 1991 LDG LCN2 3934 LDG LTF 4057 LDG MPO 4353 LDG OLFM4 10562 LDG RNASE3 6037 LDG HLA-DMA 3108 MHC II HLA-DMB 3109 MHC II HLA-DPA1 3113 MHC II HLA-DPB1 3115 MHC II HLA-DPB2 3116 MHC II HLA-DQA1 3117 MHC II HLA-DQA2 3118 MHC II HLA-DQB1 3119 MHC II HLA-DQB2 3120 MHC II HLA-DRA 3122 MHC II HLA-DRB1 3123 MHC II HLA-DRB3 3125 MHC II HLA-DRB4 3126 MHC II HLA-DRB5 3127 MHC II HLA-DRB6 3128 MHC II C1QA 712 Mono Secreted C1QB 713 Mono Secreted C1QC 714 Mono Secreted C1RL 51279 Mono Secreted CCL2 6347 Mono Secreted CCL8 6355 Mono Secreted CXCL1 2919 Mono Secreted CXCL2 2920 Mono Secreted GRN 2896 Mono Secreted IK 3550 Mono Secreted IL18RAP 8807 Mono Secreted IL1B 3553 Mono Secreted IL1RN 3557 Mono Secreted S100A8 6279 Mono Secreted THBD 7056 Mono Secreted TNF 7124 Mono Secreted CXCL10 3627 Mono Secreted CD14 929 Monocyte Cell Surface CD300C 10871 Monocyte Cell Surface CD33 945 Monocyte Cell Surface CD68 968 Monocyte Cell Surface CLEC12A 160364 Monocyte Cell Surface CLEC4D 338339 Monocyte Cell Surface CLEC4E 26253 Monocyte Cell Surface FCGR1A 2209 Monocyte Cell Surface FCGR1B 2210 Monocyte Cell Surface FCGR3B 2215 Monocyte Cell Surface LILRA5 353514 Monocyte Cell Surface LILRA6 79168 Monocyte Cell Surface LILRB2 10288 Monocyte Cell Surface LILRB3 11025 Monocyte Cell Surface OSCAR 126014 Monocyte Cell Surface SEMA4A 64218 Monocyte Cell Surface SIGLEC1 6614 Monocyte Cell Surface C1QA 712 Monocytes C1QB 713 Monocytes C1QC 714 Monocytes C1RL 51279 Monocytes CCL2 6347 Monocytes CCL8 6355 Monocytes CD14 929 Monocytes CD300C 10871 Monocytes CD33 945 Monocytes CD68 968 Monocytes CLEC12A 160364 Monocytes CLEC4D 338339 Monocytes CLEC4E 26253 Monocytes CXCL1 2919 Monocytes CXCL2 2920 Monocytes CXCR2 3579 Monocytes FCGR1A 2209 Monocytes FCGR1B 2210 Monocytes FCGR1B 2215 Monocytes GRN 2896 Monocytes IK 3550 Monocytes IL18RAP 8807 Monocytes IL1B 3553 Monocytes IL1RN 3557 Monocytes LILRA5 353514 Monocytes LILRA6 79168 Monocytes LILRB2 10288 Monocytes LILRB3 11025 Monocytes OSCAR 126014 Monocytes S100A8 6279 Monocytes SEMA4A 64218 Monocytes SIGLEC1 6614 Monocytes THBD 7056 Monocytes BST1 683 Monocytes C1R 715 Monocytes CD163 9332 Monocytes CSF2 1437 Monocytes FUT4 2526 Monocytes MNDA 4332 Monocytes MRC1 4360 Monocytes KLRF1 51348 NK NCAM1 4684 NK NCR1 9437 NK NCR3 259197 NK SH2D1B 117157 NK CLEC4C 170482 pDC NRP1 8829 pDC IGHV4-28 28400 Plasma Cells IGHV4-34 28395 Plasma Cells IGHD 3495 Plasma Cells IGHG1 3500 Plasma Cells IGHV2-5 28457 Plasma Cells IGHV3-20 28445 Plasma Cells IGHV3-23 28442 Plasma Cells IGKC 3514 Plasma Cells IGLV1-40 28825 Plasma Cells IGLV3-1 28809 Plasma Cells IGLV3-19 28797 Plasma Cells IGLV3-25 28793 Plasma Cells IGLV4-3 28786 Plasma Cells IGLV4-60 28785 Plasma Cells IGLV5-45 28781 Plasma Cells IGLV6-57 28778 Plasma Cells IGLVI-70 28763 Plasma Cells C19orf10 56005 Plasma Cells IGH 3492 Plasma Cells IGHMBP2 3508 Plasma Cells IGHV4-31 28396 Plasma Cells IGK 50802 Plasma Cells IGL 3535 Plasma Cells IGLJ3 28831 Plasma Cells IGLL1 3543 Plasma Cells IGLV@ 3546 Plasma Cells IGLV1-44 28823 Plasma Cells IGLV2-14 28815 Plasma Cells IGLV2-5 28818 Plasma Cells MZB1 51237 Plasma Cells PRDM1 639 Plasma Cells SDC1 6382 Plasma Cells THEMIS2 9473 Plasma Cells TNFRSF17 608 Plasma Cells GP1BA 2811 Platelets GP5 2814 Platelets GP6 51206 Platelets GP9 2815 Platelets LY6G6D 58530 Platelets MMRN1 22915 Platelets PEAR1 375033 Platelets PF4 5196 Platelets PF4V1 5197 Platelets PPBP 5473 Platelets SLC35D3 340146 Platelets RNU4ATAC 100151683 SNOR LOW Down SNORA11 677799 SNOR LOW Down SNORA16A 692073 SNOR LOW Down SNORA23 677808 SNOR LOW Down SNORA38B 100124536 SNOR LOW Down SNORA73A 6080 SNOR LOW Down SNORA73B 26768 SNOR LOW Down FCGR1A 2209 SNOR LOW Up CEACAM1 634 SNOR LOW Up LGALS1 3956 SNOR LOW Up SNORD24 26820 SNOR LOW Up SNORD44 26806 SNOR LOW Up SNORD47 26802 SNOR LOW Up SNORD80 26774 SNOR LOW Up CD8A 925 T Cells CD8B 926 T Cells TRDC 28526 T Cells CCR3 1232 T Cells CD226 10666 T Cells CD247 919 T Cells CD28 940 T Cells CD3D 915 T Cells CD3E 916 T Cells CD3G 917 T Cells CD4 920 T Cells CD5 921 T Cells ETS1 2113 T Cells GATA3 2625 T Cells GRAP2 9402 T Cells LEF1 51176 T Cells SH2D1A 4068 T Cells TRAC 28755 T Cells TRBC1 28639 T Cells FOXP3 50943 T reg IKZF2 22807 T reg FAS LG 356 Tactivated TAGAP 117289 Tactivated CD40LG 959 Tactivated CREM 1390 Tactivated IL17A 3605 Tactivated IL17F 112744 Tactivated IL23R 149233 Tactivated JAKMIP1 152789 Tactivated KCNA3 3738 Tactivated KCNN4 3783 Tactivated P2RX5 5026 Tactivated PRKCQ 5588 Tactivated RELT 84957 Tactivated RNF125 54941 Tactivated SATB1 6304 Tactivated TNFRSF4 7293 Tactivated TNFRSF9 3604 Tactivated TRAV10 28676 TCRA TRAV1-1 28693 TCRA TRAV1-2 28692 TCRA TRAV12-1 28674 TCRA TRAV12-2 28673 TCRA TRAV12-3 28672 TCRA TRAV13-1 28671 TCRA TRAV13-2 28670 TCRA TRAV14DV4 28669 TCRA TRAV16 28667 TCRA TRAV17 28666 TCRA TRAV18 28665 TCRA TRAV19 28664 TCRA TRAV2 28691 TCRA TRAV20 28663 TCRA TRAV21 28662 TCRA TRAV22 28661 TCRA TRAV23DV6 28660 TCRA TRAV24 28659 TCRA TRAV25 28658 TCRA TRAV26-1 28657 TCRA TRAV26-2 28656 TCRA TRAV27 28655 TCRA TRAV29DV5 28653 TCRA TRAV3 28690 TCRA TRAV30 28652 TCRA TRAV34 28648 TCRA TRAV35 28647 TCRA TRAV36DV7 28646 TCRA TRAV38-1 28644 TCRA TRAV38- 28643 TCRA 2DV8 TRAV39 28642 TCRA TRAV4 28689 TCRA TRAV40 28641 TCRA TRAV41 28640 TCRA TRAV5 28688 TCRA TRAV7 28686 TCRA TRAV8-1 28685 TCRA TRAV8-2 28684 TCRA TRAV8-3 28683 TCRA TRAV8-4 28682 TCRA TRAV8-6 28680 TCRA TRAV8-7 28679 TCRA TRAV9-1 28678 TCRA TRAV9-2 28677 TCRA TRAJ10 28745 TCRAJ TRAJ11 28744 TCRAJ TRAJ12 28743 TCRAJ TRAJ13 28742 TCRAJ TRAJ14 28741 TCRAJ TRAJ15 28740 TCRAJ TRAJ16 28739 TCRAJ TRAJ17 28738 TCRAJ TRAJ18 28737 TCRAJ TRAJ19 28736 TCRAJ TRAJ20 28735 TCRAJ TRAJ21 28734 TCRAJ TRAJ22 28733 TCRAJ TRAJ23 28732 TCRAJ TRAJ24 28731 TCRAJ TRAJ25 28730 TCRAJ TRAJ26 28729 TCRAJ TRAJ27 28728 TCRAJ TRAJ28 28727 TCRAJ TRAJ29 28726 TCRAJ TRAJ3 28752 TCRAJ TRAJ30 28725 TCRAJ TRAJ31 28724 TCRAJ TRAJ32 28723 TCRAJ TRAJ33 28722 TCRAJ TRAJ34 28721 TCRAJ TRAJ35 28720 TCRAJ TRAJ36 28719 TCRAJ TRAJ37 28718 TCRAJ TRAJ38 28717 TCRAJ TRAJ39 28716 TCRAJ TRAJ4 28751 TCRAJ TRAJ40 28715 TCRAJ TRAJ41 28714 TCRAJ TRAJ42 28713 TCRAJ TRAJ43 28712 TCRAJ TRAJ44 28711 TCRAJ TRAJ45 28710 TCRAJ TRAJ46 28709 TCRAJ TRAJ47 28708 TCRAJ TRAJ48 28707 TCRAJ TRAJ49 28706 TCRAJ TRAJ5 28750 TCRAJ TRAJ50 28705 TCRAJ TRAJ52 28703 TCRAJ TRAJ53 28702 TCRAJ TRAJ54 28701 TCRAJ TRAJ56 28699 TCRAJ TRAJ57 28698 TCRAJ TRAJ58 28697 TCRAJ TRAJ59 28696 TCRAJ TRAJ6 28749 TCRAJ TRAJ61 28694 TCRAJ TRAJ7 28748 TCRAJ TRAJ8 28747 TCRAJ TRAJ9 28746 TCRAJ TRBC2 28638 TCRB TRBJ2-1 28629 TCRB TRBJ2-2 28628 TCRB TRBJ2-2P 28627 TCRB TRBJ2-3 28626 TCRB TRBJ2-4 28625 TCRB TRBJ2-5 28624 TCRB TRBJ2-6 28623 TCRB TRBJ2-7 28622 TCRB TRBV1 28621 TCRB TRBV10-1 28585 TCRB TRBV10-2 28584 TCRB TRBV11-1 28582 TCRB TRBV11-2 28581 TCRB TRBV19 28568 TCRB TRBV2 28620 TCRB TRBV20-1 28567 TCRB TRBV21-1 28566 TCRB TRBV23-1 28564 TCRB TRBV24-1 28563 TCRB TRBV25-1 28562 TCRB TRBV27 28560 TCRB TRBV28 28559 TCRB TRBV3-1 28619 TCRB TRBV4-1 28617 TCRB TRBV4-2 28616 TCRB TRBV5-1 28614 TCRB TRBV5-3 28612 TCRB TRBV5-4 28611 TCRB TRBV5-5 28610 TCRB TRBV5-6 28609 TCRB TRBV5-7 28608 TCRB TRBV6-1 28606 TCRB TRBV6-4 28603 TCRB TRBV6-5 28602 TCRB TRBV6-6 28601 TCRB TRBV6-7 28600 TCRB TRBV6-8 28599 TCRB TRBV7-1 28597 TCRB TRBV7-3 28595 TCRB TRBV7-4 28594 TCRB TRBV7-5 28593 TCRB TRBV7-6 28592 TCRB TRBV7-7 28591 TCRB TRBV9 28586 TCRB TRDC 28526 TCRD TRDJ1 28522 TCRD TRDJ2 28521 TCRD TRDJ3 28520 TCRD TRDJ4 28519 TCRD TRDV1 28518 TCRD TRDV2 28517 TCRD TRDV3 28516 TCRD TRGC2 6967 TCRG TRGV1 6973 TCRG TRGV10 6984 TCRG TRGV11 6985 TCRG TRGV2 6974 TCRG TRGV3 6976 TCRG TRGV4 6977 TCRG TRGV5 6978 TCRG TRGV7 6981 TCRG TRGV8 6982 TCRG TRGV9 6983 TCRG BRCA1 672 TNF_Waddel Up CASP1 834 TNF_Waddel Up CXCL1 2919 TNF_Waddel Up CXCL2 2920 TNF_Waddel Up GBP1 2633 TNF_Waddel Up GP1BA 2811 TNF_Waddel Up IFI44 10561 TNF_Waddel Up IL18 3606 TNF_Waddel Up IL1B 3553 TNF_Waddel Up IL1RN 3557 TNF_Waddel Up MX1 4599 TNF_Waddel Up NAMPT 10135 TNF_Waddel Up NR3C1 2908 TNF_Waddel Up OAS3 4940 TNF_Waddel Up PATJ 10207 TNF_Waddel Up SH3BP5 9467 TNF_Waddel Up TAP2 6891 TNF_Waddel Up TNF 7124 TNF_Waddel Up TNFAIP3 7128 TNF_Waddel Up TNFRSF11A 8792 TNF_Waddel Up WT1 7490 TNF_Waddel Up ACLY 47 TNF_Waddel Up ACSL1 2180 TNF_Waddel Up ADGRE2 30817 TNF_Waddel Up AK3 50808 TNF_Waddel Up AKAP10 11216 TNF_Waddel Up AMPD3 272 TNF_Waddel Up APOL3 80833 TNF_Waddel Up ARID3A 1820 TNF_Waddel Up ARSE 415 TNF_Waddel Up ASAP1 50807 TNF_Waddel Up B4GALT5 9334 TNF_Waddel Up BCL2A1 597 TNF_Waddel Up BHLHE41 79365 TNF_Waddel Up BHMT 635 TNF_Waddel Up BIRC3 330 TNF_Waddel Up CALD1 800 TNF_Waddel Up CASP10 843 TNF_Waddel Up CCL15 6359 TNF_Waddel Up CCL20 6364 TNF_Waddel Up CCL23 6368 TNF_Waddel Up CCL3L1 6349 TNF_Waddel Up CD37 951 TNF_Waddel Up CD38 952 TNF_Waddel Up CD83 9308 TNF_Waddel Up CDKN3 1033 TNF_Waddel Up CKB 1152 TNF_Waddel Up CR2 1380 TNF_Waddel Up CTNND2 1501 TNF_Waddel Up CXCL3 2921 TNF_Waddel Up CXCL8 3576 TNF_Waddel Up CYP27B1 1594 TNF_Waddel Up DAB2 1601 TNF_Waddel Up EBI3 10148 TNF_Waddel Up EGR1 1958 TNF_Waddel Up EGR2 1959 TNF_Waddel Up EPB41 2035 TNF_Waddel Up EREG 2069 TNF_Waddel Up ETAA1 54465 TNF_Waddel Up F3 2152 TNF_Waddel Up FABP1 2168 TNF_Waddel Up FBXL2 25827 TNF_Waddel Up FCER2 2208 TNF_Waddel Up FCGR2A 2212 TNF_Waddel Up FLJ11129 54674 TNF_Waddel Up FLNA 2316 TNF_Waddel Up G0S2 50486 TNF_Waddel Up GCH1 2643 TNF_Waddel Up GJB2 2706 TNF_Waddel Up GLS 2744 TNF_Waddel Up GMIP 51291 TNF_Waddel Up GRK3 157 TNF_Waddel Up HCAR3 8843 TNF_Waddel Up HHEX 3087 TNF_Waddel Up HOMER2 9455 TNF_Waddel Up HP 3240 TNF_Waddel Up ICAM1 3383 TNF_Waddel Up IDO1 3620 TNF_Waddel Up IKBKG 8517 TNF_Waddel Up IL16 3603 TNF_Waddel Up IL1A 3552 TNF_Waddel Up IL6 3569 TNF_Waddel Up INHBA 3624 TNF_Waddel Up INSIG1 3638 TNF_Waddel Up ITGA6 3655 TNF_Waddel Up KITLG 4254 TNF_Waddel Up KLF1 10661 TNF_Waddel Up KMO 8564 TNF_Waddel Up LGALS3BP 3959 TNF_Waddel Up MAP3K4 4216 TNF_Waddel Up MARCKS 4082 TNF_Waddel Up MGLL 11343 TNF_Waddel Up MMP19 4327 TNF_Waddel Up MN1 4330 TNF_Waddel Up MRPS15 64960 TNF_Waddel Up MSC 9242 TNF_Waddel Up MTF1 4520 TNF_Waddel Up NELL2 4753 TNF_Waddel Up NFKB1 4790 TNF_Waddel Up NFKB2 4791 TNF_Waddel Up NFKBIA 4792 TNF_Waddel Up NFKBIZ 64332 TNF_Waddel Up NKX3-2 579 TNF_Waddel Up PDE4DIP 9659 TNF_Waddel Up PDPN 10630 TNF_Waddel Up PIAS4 51588 TNF_Waddel Up PLAUR 5329 TNF_Waddel Up PTGES 9536 TNF_Waddel Up PTGS2 5743 TNF_Waddel Up RELB 5971 TNF_Waddel Up RPGR 6103 TNF_Waddel Up RPS9 6203 TNF_Waddel Up SDC4 6385 TNF_Waddel Up SERPIND1 3053 TNF_Waddel Up SFRP1 6422 TNF_Waddel Up SLAMF1 6504 TNF_Waddel Up SLC30A4 7782 TNF_Waddel Up SOD2 6648 TNF_Waddel Up SPI1 6688 TNF_Waddel Up SSPN 8082 TNF_Waddel Up STAT4 6775 TNF_Waddel Up TAF15 8148 TNF_Waddel Up TBX3 6926 TNF_Waddel Up TFF1 7031 TNF_Waddel Up TNFAIP2 7127 TNF_Waddel Up TRAF1 7185 TNF_Waddel Up TSC22D1 8848 TNF_Waddel Up TYROBP 7305 TNF_Waddel Up UBE2C 11065 TNF_Waddel Up VEGFA 7422 TNF_Waddel Up B4GALT3 8703 Unfolded Protein CALR 811 Unfolded Protein CALU 813 Unfolded Protein CANX 821 Unfolded Protein CDS2 8760 Unfolded Protein CHST12 55501 Unfolded Protein CHST2 9435 Unfolded Protein DERL1 79139 Unfolded Protein DERL2 51009 Unfolded Protein DNAJC3 5611 Unfolded Protein EDEM2 55741 Unfolded Protein EDEM3 80267 Unfolded Protein EMC9 51016 Unfolded Protein ERAP1 51752 Unfolded Protein ERGIC2 51290 Unfolded Protein ERO1L 30001 Unfolded Protein EXT1 2131 Unfolded Protein GALNT2 2590 Unfolded Protein GOLT1B 51026 Unfolded Protein HERPUD1 9709 Unfolded Protein HYOU1 10525 Unfolded Protein IER3IP1 51124 Unfolded Protein IMPAD1 54928 Unfolded Protein KDELC1 79070 Unfolded Protein KDELR2 11014 Unfolded Protein LMAN2 10960 Unfolded Protein LPGAT1 9926 Unfolded Protein MAN1A1 4121 Unfolded Protein MANEA 79694 Unfolded Protein MANF 7873 Unfolded Protein NUCB2 4925 Unfolded Protein PDIA4 9601 Unfolded Protein PDIA6 10130 Unfolded Protein PIGK 10026 Unfolded Protein PPIB 5479 Unfolded Protein SEC24D 9871 Unfolded Protein SEC61G 23480 Unfolded Protein SPCS3 60559 Unfolded Protein SSR1 6745 Unfolded Protein SSR3 6747 Unfolded Protein TRAM1 23471 Unfolded Protein TRAM2 9697 Unfolded Protein UGGT1 56886 Unfolded Protein XBP1 7494 Unfolded Protein APP 351 NLRP3 Inflammasome ATAT1 79969 NLRP3 Inflammasome CARD8 22900 NLRP3 Inflammasome CASP1 834 NLRP3 Inflammasome CASP4 837 NLRP3 Inflammasome CD36 948 NLRP3 Inflammasome CPTP 80772 NLRP3 Inflammasome DHX33 56919 NLRP3 Inflammasome EIF2AK2 5610 NLRP3 Inflammasome GBP5 115362 NLRP3 Inflammasome GSDMD 79792 NLRP3 Inflammasome HSP90AB1 3326 NLRP3 Inflammasome MEFV 4210 NLRP3 Inflammasome NFKB1 4790 NLRP3 Inflammasome NFKB2 4791 NLRP3 Inflammasome NLRC3 197358 NLRP3 Inflammasome NLRP3 114548 NLRP3 Inflammasome P2RX7 5027 NLRP3 Inflammasome PANX1 24145 NLRP3 Inflammasome PSTPIP1 9051 NLRP3 Inflammasome PYCARD 29108 NLRP3 Inflammasome PYDC2 152138 NLRP3 Inflammasome RELA 5970 NLRP3 Inflammasome SIRT2 22933 NLRP3 Inflammasome SUGT1 10910 NLRP3 Inflammasome TLR4 7099 NLRP3 Inflammasome TLR6 10333 NLRP3 Inflammasome TXN 7295 NLRP3 Inflammasome TXNIP 10628 NLRP3 Inflammasome USP50 373509 NLRP3 Inflammasome C1QA 712 Classical Complement Pathway C1QB 713 Classical Complement Pathway C1QC 714 Classical Complement Pathway C1R 715 Classical Complement Pathway C1S 716 Classical Complement Pathway C2 717 Classical Complement Pathway C3 718 Classical Complement Pathway C4A 720 Classical Complement Pathway C4B 721 Classical Complement Pathway C4B_2 100293534 Classical Complement Pathway C5 727 Classical Complement Pathway C6 729 Classical Complement Pathway C7 730 Classical Complement Pathway C8A 731 Classical Complement Pathway C9 735 Classical Complement Pathway C3 718 Alternative Complement Pathway C5 727 Alternative Complement Pathway C6 729 Alternative Complement Pathway C7 730 Alternative Complement Pathway C8A 731 Alternative Complement Pathway C9 735 Alternative Complement Pathway CFB 629 Alternative Complement Pathway CFD 1675 Alternative Complement Pathway CFH 3075 Alternative Complement Pathway CFHR5 81494 Alternative Complement Pathway CFP 5199 Alternative Complement Pathway CR1 1378 Alternative Complement Pathway GZMM 3004 Alternative Complement Pathway MIR520B 574473 Alternative Complement Pathway MIR520E 574461 Alternative Complement Pathway VSIG4 11326 Alternative Complement Pathway A2M 2 Lectin-Induced Complement Pathway C2 717 Lectin-Induced Complement Pathway C3 718 Lectin-Induced Complement Pathway C4A 720 Lectin-Induced Complement Pathway C4B 721 Lectin-Induced Complement Pathway C4B_2 100293534 Lectin-Induced Complement Pathway C5 727 Lectin-Induced Complement Pathway C6 729 Lectin-Induced Complement Pathway C7 730 Lectin-Induced Complement Pathway C8A 731 Lectin-Induced Complement Pathway C9 735 Lectin-Induced Complement Pathway COLEC10 10584 Lectin-Induced Complement Pathway COLEC11 78989 Lectin-Induced Complement Pathway FCN1 2219 Lectin-Induced Complement Pathway FCN2 2220 Lectin-Induced Complement Pathway FCN3 8547 Lectin-Induced Complement Pathway KRT1 3848 Lectin-Induced Complement Pathway MASP1 5648 Lectin-Induced Complement Pathway MASP2 10747 Lectin-Induced Complement Pathway MBL2 4153 Lectin-Induced Complement Pathway SERPING1 710 Lectin-Induced Complement Pathway

Table of NLRP3 Inflamm and Complement geneSymbol geneEntrezID GeneSet APP 351 NLRP3 Inflammasome ATAT1 79969 NLRP3 Inflammasome CARD8 22900 NLRP3 Inflammasome CASP1 834 NLRP3 Inflammasome CASP4 837 NLRP3 Inflammasome CD36 948 NLRP3 Inflammasome CPTP 80772 NLRP3 Inflammasome DHX33 56919 NLRP3 Inflammasome EIF2AK2 5610 NLRP3 Inflammasome GBP5 115362 NLRP3 Inflammasome GSDMD 79792 NLRP3 Inflammasome HSP90AB1 3326 NLRP3 Inflammasome MEFV 4210 NLRP3 Inflammasome NFKB1 4790 NLRP3 Inflammasome NFKB2 4791 NLRP3 Inflammasome NLRC3 197358 NLRP3 Inflammasome NLRP3 114548 NLRP3 Inflammasome P2RX7 5027 NLRP3 Inflammasome PANX1 24145 NLRP3 Inflammasome PSTPIP1 9051 NLRP3 Inflammasome PYCARD 29108 NLRP3 Inflammasome PYDC2 152138 NLRP3 Inflammasome RELA 5970 NLRP3 Inflammasome SIRT2 22933 NLRP3 Inflammasome SUGT1 10910 NLRP3 Inflammasome TLR4 7099 NLRP3 Inflammasome TLR6 10333 NLRP3 Inflammasome TXN 7295 NLRP3 Inflammasome TXNIP 10628 NLRP3 Inflammasome USP50 373509 NLRP3 Inflammasome C1QA 712 Classical Complement Pathway CIQB 713 Classical Complement Pathway C1QC 714 Classical Complement Pathway C1R 715 Classical Complement Pathway C1S 716 Classical Complement Pathway C2 717 Classical Complement Pathway C3 718 Classical Complement Pathway C4A 720 Classical Complement Pathway C4B 721 Classical Complement Pathway C4B_2 100293534 Classical Complement Pathway C5 727 Classical Complement Pathway C6 729 Classical Complement Pathway C7 730 Classical Complement Pathway C8A 731 Classical Complement Pathway C9 735 Classical Complement Pathway C3 718 Alternative Complement Pathway C5 727 Alternative Complement Pathway C6 729 Alternative Complement Pathway C7 730 Alternative Complement Pathway C8A 731 Alternative Complement Pathway C9 735 Alternative Complement Pathway CFB 629 Alternative Complement Pathway CFD 1675 Alternative Complement Pathway CFH 3075 Alternative Complement Pathway CFHR5 81494 Alternative Complement Pathway CFP 5199 Alternative Complement Pathway CR1 1378 Alternative Complement Pathway GZMM 3004 Alternative Complement Pathway MIR520B 574473 Alternative Complement Pathway MIR520E 574461 Alternative Complement Pathway VSIG4 11326 Alternative Complement Pathway A2M 2 Lectin-Induced Complement Pathway C2 717 Lectin-Induced Complement Pathway C3 718 Lectin-Induced Complement Pathway C4A 720 Lectin-Induced Complement Pathway C4B 721 Lectin-Induced Complement Pathway C4B_2 100293534 Lectin-Induced Complement Pathway C5 727 Lectin-Induced Complement Pathway C6 729 Lectin-Induced Complement Pathway C7 730 Lectin-Induced Complement Pathway C8A 731 Lectin-Induced Complement Pathway C9 735 Lectin-Induced Complement Pathway COLEC10 10584 Lectin-Induced Complement Pathway COLEC11 78989 Lectin-Induced Complement Pathway FCN1 2219 Lectin-Induced Complement Pathway FCN2 2220 Lectin-Induced Complement Pathway FCN3 8547 Lectin-Induced Complement Pathway KRT1 3848 Lectin-Induced Complement Pathway MASP1 5648 Lectin-Induced Complement Pathway MASP2 10747 Lectin-Induced Complement Pathway MBL2 4153 Lectin-Induced Complement Pathway SERPING1 710 Lectin-Induced Complement Pathway

Table of IL6-IL1 geneSymbol geneEntrezID GeneSet IL1A 3552 Proinflammatory IL-1 Family IL1B 3553 Proinflammatory IL-1 Family IL18 3606 Proinflammatory IL-1 Family IL36A 27179 Proinflammatory IL-1 Family IL36B 27177 Proinflammatory IL-1 Family IL36G 56300 Proinflammatory IL-1 Family IL33 90865 Proinflammatory IL-1 Family IL1R1 3554 Proinflammatory IL-1 Family IL1RAP 3556 Proinflammatory IL-1 Family IL18R1 8809 Proinflammatory IL-1 Family IL18RAP 8807 Proinflammatory IL-1 Family IL6 3569 IL-6R Complex IL6R 3570 IL-6R Complex IL6ST 3572 IL-6R Complex

Table of M1 and M2 Macrophages geneSymbol geneEntrezID GeneSet AK3 50808 M1 APOL1 8542 M1 APOL2 23780 M1 APOL3 80833 M1 APOL6 80830 M1 ATF3 467 M1 BCL2A1 597 M1 BIRC3 330 M1 CCL15 6359 M1 CCL19 6363 M1 CCL20 6364 M1 CCL5 6352 M1 CCR7 1236 M1 CHI3L2 1117 M1 CXCL10 3627 M1 CXCL11 6373 M1 CXCL9 4283 M1 EDN1 1906 M1 FAS 355 M1 GADD45G 10912 M1 HESX1 8820 M1 HSD11B1 3290 M1 IDO1 3620 M1 IGFBP4 3487 M1 IL12B 3593 M1 IL15 3600 M1 IL15RA 3601 M1 IL2RA 3559 M1 IL6 3569 M1 IL7R 3575 M1 INHBA 3624 M1 IRF1 3659 M1 IRF7 3665 M1 NAMPT 10135 M1 OAS2 4939 M1 OASL 8638 M1 PDGFA 5154 M1 PFKFB3 5209 M1 PFKP 5214 M1 PLA1A 51365 M1 PSMA2 5683 M1 PSMB9 5698 M1 PSME2 5721 M1 PTX3 5806 M1 SCO2 9997 M1 SLC2A6 11182 M1 SLC31A2 1318 M1 SLC7A5 8140 M1 SLCO5A1 81796 M1 SPHK1 8877 M1 TNF 7124 M1 TNFSF10 8743 M1 VCAN 1462 M1 XAF1 54739 M1 ADK 132 M2 ALOX15 246 M2 CA2 760 M2 CCL13 6357 M2 CCL18 6362 M2 CCL23 6368 M2 CD209 30835 M2 CD36 948 M2 CERK 64781 M2 CHN2 1124 M2 CLEC4F 165530 M2 CLEC7A 64581 M2 CTSC 1075 M2 CXCR4 7852 M2 DLC1 10395 M2 EGR2 1959 M2 FGL2 10875 M2 FN1 2335 M2 GAS7 8522 M2 HEXB 3074 M2 HNMT 3176 M2 HRH1 3269 M2 HS3ST1 9957 M2 HS3ST2 9956 M2 IGF1 3479 M2 LIPA 3988 M2 LPAR6 10161 M2 LTA4H 4048 M2 MAF 4094 M2 MRC1 4360 M2 MS4A4A 51338 M2 MS4A6A 64231 M2 MSR1 4481 M2 P2RY13 53829 M2 P2RY14 9934 M2 SELENOP 6414 M2 SLC38A6 145389 M2 SLC4A7 9497 M2 SLCO2B1 11309 M2 TGFBI 7045 M2 TGFBR2 7048 M2 TLR5 7100 M2 TPST2 8459 M2

Table of Kotliarov et al. CD 40 geneSymbol geneEntrezID GeneSet BUB1B 701 CD40act CCL22 6367 CD40act CD58 965 CD40act DBI 1622 CD40act DUSP4 1846 CD40act FABP5 2171 CD40act FDPS 2224 CD40act FEN1 2237 CD40act GAPDH 2597 CD40act GARS 2617 CD40act GRHPR 9380 CD40act H2AFX 3014 CD40act H2AFZ 3015 CD40act HMGB2 3148 CD40act HMMR 3161 CD40act HPRT1 3251 CD40act IMPDH2 3615 CD40act LDHA 3939 CD40act LDHB 3945 CD40act LMNB1 4001 CD40act LPXN 9404 CD40act MCM2 4171 CD40act MCM3 4172 CD40act MCM6 4175 CD40act MSH6 2956 CD40act MTHFD2 10797 CD40act MYBL2 4605 CD40act NDC80 10403 CD40act NME1 4830 CD40act PAICS 10606 CD40act PCNA 5111 CD40act PKM 5315 CD40act PRDX3 10935 CD40act RFTN1 23180 CD40act RGS10 6001 CD40act SLAMF1 6504 CD40act TK1 7083 CD40act TOP2A 7153 CD40act TPX2 22974 CD40act TRAF1 7185 CD40act TUBA1B 10376 CD40act TXN 7295 CD40act TYMS 7298 CD40act UBE2S 27338 CD40act VDAC1 7416 CD40act WEE1 7465 CD40act WSB2 55884 CD40act ZWINT 11130 CD40act

Table of Interferons (IFN) geneSymbol geneEntrezID GeneSet ACSL1 2180 IFNA2 Signature ADAR 103 IFNA2 Signature AGT 183 IFNA2 Signature AIM2 9447 IFNA2 Signature AKAP2 11217 IFNA2 Signature APOBEC3B 9582 IFNA2 Signature APOBEC3G 60489 IFNA2 Signature APOL3 80833 IFNA2 Signature ATF3 467 IFNA2 Signature ATF5 22809 IFNA2 Signature BAG1 573 IFNA2 Signature BARD1 580 IFNA2 Signature BCL7B 9275 IFNA2 Signature BLVRA 644 IFNA2 Signature BRCA1 672 IFNA2 Signature BRCA2 675 IFNA2 Signature BST2 684 IFNA2 Signature BUB1 699 IFNA2 Signature C2 717 IFNA2 Signature CACNA1A 773 IFNA2 Signature CAD 790 IFNA2 Signature CAMK2A 815 IFNA2 Signature CASP1 834 IFNA2 Signature CASP10 843 IFNA2 Signature CASP5 838 IFNA2 Signature CBR1 873 IFNA2 Signature CBWD1 55871 IFNA2 Signature CCL13 6357 IFNA2 Signature CCL7 6354 IFNA2 Signature CCL8 6355 IFNA2 Signature CCNA1 8900 IFNA2 Signature CCND2 894 IFNA2 Signature CD2AP 23607 IFNA2 Signature CD38 952 IFNA2 Signature CD4 920 IFNA2 Signature CD69 969 IFNA2 Signature CDC42EP1 11135 IFNA2 Signature CDK4 1019 IFNA2 Signature CDKN1A 1026 IFNA2 Signature CFB 629 IFNA2 Signature CH25H 9023 IFNA2 Signature CHKA 1119 IFNA2 Signature CNTN6 27255 IFNA2 Signature COL3A1 1281 IFNA2 Signature CTSL 1514 IFNA2 Signature CXCL10 3627 IFNA2 Signature CXCL11 6373 IFNA2 Signature CXCL9 4283 IFNA2 Signature CXCR2 3579 IFNA2 Signature CYP2J2 1573 IFNA2 Signature DAB2 1601 IFNA2 Signature DEFB1 1672 IFNA2 Signature DLL1 28514 IFNA2 Signature DSC2 1824 IFNA2 Signature DUSP5 1847 IFNA2 Signature DUSP7 1849 IFNA2 Signature DYNLT1 6993 IFNA2 Signature DYSF 8291 IFNA2 Signature ECE1 1889 IFNA2 Signature EDN1 1906 IFNA2 Signature EIF2AK2 5610 IFNA2 Signature EIF2B1 1967 IFNA2 Signature EIF4ENIF1 56478 IFNA2 Signature ENPP2 5168 IFNA2 Signature EPB41 2035 IFNA2 Signature ETV4 2118 IFNA2 Signature F8 2157 IFNA2 Signature FAF1 11124 IFNA2 Signature FAS 355 IFNA2 Signature FGF1 2246 IFNA2 Signature FLNA 2316 IFNA2 Signature FOXO1 2308 IFNA2 Signature FTL 2512 IFNA2 Signature FUT4 2526 IFNA2 Signature GADD45B 4616 IFNA2 Signature GBAP1 2630 IFNA2 Signature GBP1 2633 IFNA2 Signature GBP2 2634 IFNA2 Signature GCH1 2643 IFNA2 Signature GCNT1 2650 IFNA2 Signature GLB1 2720 IFNA2 Signature GLS 2744 IFNA2 Signature GMPR 2766 IFNA2 Signature GPR161 23432 IFNA2 Signature GUK1 2987 IFNA2 Signature HBG2 3048 IFNA2 Signature HCAR3 8843 IFNA2 Signature HIST2H2AA3 8337 IFNA2 Signature HLA-DOA 3111 IFNA2 Signature HLA-DRB5 3127 IFNA2 Signature HS6ST1 9394 IFNA2 Signature HSP90AA1 3320 IFNA2 Signature IDO1 3620 IFNA2 Signature IFI16 3428 IFNA2 Signature IFI27 3429 IFNA2 Signature IFI35 3430 IFNA2 Signature IFI44 10561 IFNA2 Signature IFI44L 10964 IFNA2 Signature IFI6 2537 IFNA2 Signature IFIT1 3434 IFNA2 Signature IFIT5 24138 IFNA2 Signature IFITM1 8519 IFNA2 Signature IFITM2 10581 IFNA2 Signature IFITM3 10410 IFNA2 Signature IFNG 3458 IFNA2 Signature IFRD1 3475 IFNA2 Signature IGL 3535 IFNA2 Signature IKBKG 8517 IFNA2 Signature IL15 3600 IFNA2 Signature IL15RA 3601 IFNA2 Signature IL1RN 3557 IFNA2 Signature IL6 3569 IFNA2 Signature INPPL1 3636 IFNA2 Signature IRF2 3660 IFNA2 Signature IRF7 3665 IFNA2 Signature ISG15 9636 IFNA2 Signature ISG20 3669 IFNA2 Signature ITIH2 3698 IFNA2 Signature JAK2 3717 IFNA2 Signature JUP 3728 IFNA2 Signature KCNA3 3738 IFNA2 Signature KDELR2 11014 IFNA2 Signature KIF20B 9585 IFNA2 Signature KLF6 1316 IFNA2 Signature KPNB1 3837 IFNA2 Signature KRT8 3856 IFNA2 Signature LAG3 3902 IFNA2 Signature LAMP3 27074 IFNA2 Signature LAP3 51056 IFNA2 Signature LEPR 3953 IFNA2 Signature LGALS2 3957 IFNA2 Signature LGALS3BP 3959 IFNA2 Signature LGALS9 3965 IFNA2 Signature LGMN 5641 IFNA2 Signature LMNB1 4001 IFNA2 Signature LMO2 4005 IFNA2 Signature LY6E 4061 IFNA2 Signature MAP2K5 5607 IFNA2 Signature MCL1 4170 IFNA2 Signature MED1 5469 IFNA2 Signature MGLL 11343 IFNA2 Signature MMP16 4325 IFNA2 Signature MNDA 4332 IFNA2 Signature MRPS15 64960 IFNA2 Signature MSR1 4481 IFNA2 Signature MX1 4599 IFNA2 Signature MX2 4600 IFNA2 Signature MYD88 4615 IFNA2 Signature NAMPT 10135 IFNA2 Signature NFE2L3 9603 IFNA2 Signature NKTR 4820 IFNA2 Signature NMI 9111 IFNA2 Signature NR3C1 2908 IFNA2 Signature NUB1 51667 IFNA2 Signature NUPR1 26471 IFNA2 Signature OAS1 4938 IFNA2 Signature OAS2 4939 IFNA2 Signature OAS3 4940 IFNA2 Signature OSBPL1A 114876 IFNA2 Signature PATJ 10207 IFNA2 Signature PDGFB 5155 IFNA2 Signature PDGFRL 5157 IFNA2 Signature PGGT1B 5229 IFNA2 Signature PKD2 5311 IFNA2 Signature PLSCR1 5359 IFNA2 Signature PMAIP1 5366 IFNA2 Signature PML 5371 IFNA2 Signature PRKRA 8575 IFNA2 Signature PSMB9 5698 IFNA2 Signature PTCH1 5727 IFNA2 Signature RBCK1 10616 IFNA2 Signature RET 5979 IFNA2 Signature RGS1 5996 IFNA2 Signature RGS6 9628 IFNA2 Signature RPS9 6203 IFNA2 Signature RTP4 64108 IFNA2 Signature SAT1 6303 IFNA2 Signature SCARB2 950 IFNA2 Signature SERPING1 710 IFNA2 Signature SIT1 27240 IFNA2 Signature SLAMF1 6504 IFNA2 Signature SOCS1 8651 IFNA2 Signature SP100 6672 IFNA2 Signature SP110 3431 IFNA2 Signature SP140 11262 IFNA2 Signature SPIB 6689 IFNA2 Signature ST3GAL5 8869 IFNA2 Signature STAP1 26228 IFNA2 Signature STAT1 6772 IFNA2 Signature STAT2 6773 IFNA2 Signature STX11 8676 IFNA2 Signature SUPT3H 8464 IFNA2 Signature SYN2 6854 IFNA2 Signature TAF5L 27097 IFNA2 Signature TAP1 6890 IFNA2 Signature TAP2 6891 IFNA2 Signature TARBP1 6894 IFNA2 Signature TCN2 6948 IFNA2 Signature TFDP2 7029 IFNA2 Signature TGM1 7051 IFNA2 Signature TLR3 7098 IFNA2 Signature TLR7 51284 IFNA2 Signature TNFRSF11A 8792 IFNA2 Signature TNFSF10 8743 IFNA2 Signature TNFSF6 356 IFNA2 Signature TNK2 10188 IFNA2 Signature TOR1B 27348 IFNA2 Signature TRA2B 6434 IFNA2 Signature TRD 6964 IFNA2 Signature TRIM21 6737 IFNA2 Signature TRIM22 10346 IFNA2 Signature TRIM26 7726 IFNA2 Signature TRIM34 53840 IFNA2 Signature TRIM38 10475 IFNA2 Signature UBA7 7318 IFNA2 Signature UBE2L6 9246 IFNA2 Signature UBE2S 27338 IFNA2 Signature UBE3A 7337 IFNA2 Signature UNC93B1 81622 IFNA2 Signature USP18 11274 IFNA2 Signature VAMP5 10791 IFNA2 Signature WARS 7453 IFNA2 Signature WT1 7490 IFNA2 Signature XAF1 54739 IFNA2 Signature ACKR3 57007 IFNB1 ALTERNATIVE PW Increased transcripts ACOD1 730249 IFNB1 ALTERNATIVE PW Increased transcripts ADORA2B 136 IFNB1 ALTERNATIVE PW Increased transcripts AEN 64782 IFNB1 ALTERNATIVE PW Increased transcripts AMBP 259 IFNB1 ALTERNATIVE PW Increased transcripts ARG1 383 IFNB1 ALTERNATIVE PW Increased transcripts ARG2 384 IFNB1 ALTERNATIVE PW Increased transcripts ARHGAP31 57514 IFNB1 ALTERNATIVE PW Increased transcripts ASPA 443 IFNB1 ALTERNATIVE PW Increased transcripts B4GALT5 9334 IFNB1 ALTERNATIVE PW Increased transcripts BCL3 602 IFNB1 ALTERNATIVE PW Increased transcripts BYSL 705 IFNB1 ALTERNATIVE PW Increased transcripts CA13 377677 IFNB1 ALTERNATIVE PW Increased transcripts CAMKK2 10645 IFNB1 ALTERNATIVE PW Increased transcripts CCL2 6347 IFNB1 ALTERNATIVE PW Increased transcripts CCL3L3 6349 IFNB1 ALTERNATIVE PW Increased transcripts CCL4 6351 IFNB1 ALTERNATIVE PW Increased transcripts CCL7 6354 IFNB1 ALTERNATIVE PW Increased transcripts CCRL2 9034 IFNB1 ALTERNATIVE PW Increased transcripts CD14 929 IFNB1 ALTERNATIVE PW Increased transcripts CD207 50489 IFNB1 ALTERNATIVE PW Increased transcripts CD86 942 IFNB1 ALTERNATIVE PW Increased transcripts CDC42EP2 10435 IFNB1 ALTERNATIVE PW Increased transcripts CDKN1A 1026 IFNB1 ALTERNATIVE PW Increased transcripts CDR2 1039 IFNB1 ALTERNATIVE PW Increased transcripts CLEC4E 26253 IFNB1 ALTERNATIVE PW Increased transcripts CLEC6A 93978 IFNB1 ALTERNATIVE PW Increased transcripts COQ10B 80219 IFNB1 ALTERNATIVE PW Increased transcripts CRYAA 1409 IFNB1 ALTERNATIVE PW Increased transcripts CSTA 1475 IFNB1 ALTERNATIVE PW Increased transcripts CTPS1 1503 IFNB1 ALTERNATIVE PW Increased transcripts CXCL2 2920 IFNB1 ALTERNATIVE PW Increased transcripts CXCL3 2921 IFNB1 ALTERNATIVE PW Increased transcripts DNMT3L 29947 IFNB1 ALTERNATIVE PW Increased transcripts DOT1L 84444 IFNB1 ALTERNATIVE PW Increased transcripts DRAM1 55332 IFNB1 ALTERNATIVE PW Increased transcripts DUSP16 80824 IFNB1 ALTERNATIVE PW Increased transcripts EEF1E1 9521 IFNB1 ALTERNATIVE PW Increased transcripts EPHA4 2043 IFNB1 ALTERNATIVE PW Increased transcripts ETS2 2114 IFNB1 ALTERNATIVE PW Increased transcripts EXOC3L4 91828 IFNB1 ALTERNATIVE PW Increased transcripts F3 2152 IFNB1 ALTERNATIVE PW Increased transcripts FAM20C 56975 IFNB1 ALTERNATIVE PW Increased transcripts FCRL5 83416 IFNB1 ALTERNATIVE PW Increased transcripts FFAR2 2867 IFNB1 ALTERNATIVE PW Increased transcripts FMNL2 114793 IFNB1 ALTERNATIVE PW Increased transcripts FPR2 2358 IFNB1 ALTERNATIVE PW Increased transcripts GFPT1 2673 IFNB1 ALTERNATIVE PW Increased transcripts Gk 2710 IFNB1 ALTERNATIVE PW Increased transcripts GPR84 53831 IFNB1 ALTERNATIVE PW Increased transcripts GRWD1 83743 IFNB1 ALTERNATIVE PW Increased transcripts HBEGF 1839 IFNB1 ALTERNATIVE PW Increased transcripts HCAR2 338442 IFNB1 ALTERNATIVE PW Increased transcripts HEATR1 55127 IFNB1 ALTERNATIVE PW Increased transcripts HIVEP3 59269 IFNB1 ALTERNATIVE PW Increased transcripts HSPA1A 3303 IFNB1 ALTERNATIVE PW Increased transcripts HSPA1B 3304 IFNB1 ALTERNATIVE PW Increased transcripts ICAM1 3383 IFNB1 ALTERNATIVE PW Increased transcripts ID1 3397 IFNB1 ALTERNATIVE PW Increased transcripts IER3 8870 IFNB1 ALTERNATIVE PW Increased transcripts IFI16 3428 IFNB1 ALTERNATIVE PW Increased transcripts IKBKE 9641 IFNB1 ALTERNATIVE PW Increased transcripts IL1A 3552 IFNB1 ALTERNATIVE PW Increased transcripts IL1B 3553 IFNB1 ALTERNATIVE PW Increased transcripts IL1RN 3557 IFNB1 ALTERNATIVE PW Increased transcripts IL6 3569 IFNB1 ALTERNATIVE PW Increased transcripts IRAK3 11213 IFNB1 ALTERNATIVE PW Increased transcripts ITGA5 3678 IFNB1 ALTERNATIVE PW Increased transcripts ITGAX 3687 IFNB1 ALTERNATIVE PW Increased transcripts KPNA2 3838 IFNB1 ALTERNATIVE PW Increased transcripts MAFF 23764 IFNB1 ALTERNATIVE PW Increased transcripts MARCKSL1 65108 IFNB1 ALTERNATIVE PW Increased transcripts MARCO 8685 IFNB1 ALTERNATIVE PW Increased transcripts MEFV 4210 IFNB1 ALTERNATIVE PW Increased transcripts MMP14 4323 IFNB1 ALTERNATIVE PW Increased transcripts MT1A 4489 IFNB1 ALTERNATIVE PW Increased transcripts MT2A 4502 IFNB1 ALTERNATIVE PW Increased transcripts MYBPC2 4606 IFNB1 ALTERNATIVE PW Increased transcripts NAB2 4665 IFNB1 ALTERNATIVE PW Increased transcripts NOCT 25819 IFNB1 ALTERNATIVE PW Increased transcripts NOP16 51491 IFNB1 ALTERNATIVE PW Increased transcripts NOP2 4839 IFNB1 ALTERNATIVE PW Increased transcripts NR1H3 10062 IFNB1 ALTERNATIVE PW Increased transcripts NR4A1 3164 IFNB1 ALTERNATIVE PW Increased transcripts OLR1 4973 IFNB1 ALTERNATIVE PW Increased transcripts OSM 5008 IFNB1 ALTERNATIVE PW Increased transcripts PDIA6 10130 IFNB1 ALTERNATIVE PW Increased transcripts PHLDA1 22822 IFNB1 ALTERNATIVE PW Increased transcripts PHLDB1 23187 IFNB1 ALTERNATIVE PW Increased transcripts PIM1 5292 IFNB1 ALTERNATIVE PW Increased transcripts POGK 57645 IFNB1 ALTERNATIVE PW Increased transcripts PPRC1 23082 IFNB1 ALTERNATIVE PW Increased transcripts PROK2 60675 IFNB1 ALTERNATIVE PW Increased transcripts PTGES 9536 IFNB1 ALTERNATIVE PW Increased transcripts PTGIR 5739 IFNB1 ALTERNATIVE PW Increased transcripts PVR 5817 IFNB1 ALTERNATIVE PW Increased transcripts RAB20 55647 IFNB1 ALTERNATIVE PW Increased transcripts RAI14 26064 IFNB1 ALTERNATIVE PW Increased transcripts RELB 5971 IFNB1 ALTERNATIVE PW Increased transcripts RND1 27289 IFNB1 ALTERNATIVE PW Increased transcripts RRP12 23223 IFNB1 ALTERNATIVE PW Increased transcripts RRS1 23212 IFNB1 ALTERNATIVE PW Increased transcripts SAA1 6288 IFNB1 ALTERNATIVE PW Increased transcripts SCAMP1 9522 IFNB1 ALTERNATIVE PW Increased transcripts SDC4 6385 IFNB1 ALTERNATIVE PW Increased transcripts SERPINB2 5055 IFNB1 ALTERNATIVE PW Increased transcripts SERPINE1 5054 IFNB1 ALTERNATIVE PW Increased transcripts SHMT1 6470 IFNB1 ALTERNATIVE PW Increased transcripts SLAMF8 56833 IFNB1 ALTERNATIVE PW Increased transcripts SLC12A4 6560 IFNB1 ALTERNATIVE PW Increased transcripts SLC15A3 51296 IFNB1 ALTERNATIVE PW Increased transcripts SLC16A10 117247 IFNB1 ALTERNATIVE PW Increased transcripts SLC20A1 6574 IFNB1 ALTERNATIVE PW Increased transcripts SLC25A25 114789 IFNB1 ALTERNATIVE PW Increased transcripts SLC25A33 84275 IFNB1 ALTERNATIVE PW Increased transcripts SLC2A6 11182 IFNB1 ALTERNATIVE PW Increased transcripts SLC39A14 23516 IFNB1 ALTERNATIVE PW Increased transcripts SLC7A2 6542 IFNB1 ALTERNATIVE PW Increased transcripts SLC7A5 8140 IFNB1 ALTERNATIVE PW Increased transcripts SNX18 112574 IFNB1 ALTERNATIVE PW Increased transcripts SOCS3 9021 IFNB1 ALTERNATIVE PW Increased transcripts SOD2 6648 IFNB1 ALTERNATIVE PW Increased transcripts SUSD6 9766 IFNB1 ALTERNATIVE PW Increased transcripts TFEC 22797 IFNB1 ALTERNATIVE PW Increased transcripts TFRC 7037 IFNB1 ALTERNATIVE PW Increased transcripts TGM2 7052 IFNB1 ALTERNATIVE PW Increased transcripts TIMM8A 1678 IFNB1 ALTERNATIVE PW Increased transcripts TLNRD1 59274 IFNB1 ALTERNATIVE PW Increased transcripts TLR2 7097 IFNB1 ALTERNATIVE PW Increased transcripts TMA16 55319 IFNB1 ALTERNATIVE PW Increased transcripts TNF 7124 IFNB1 ALTERNATIVE PW Increased transcripts TNFAIP2 7127 IFNB1 ALTERNATIVE PW Increased transcripts TNFAIP3 7128 IFNB1 ALTERNATIVE PW Increased transcripts TNFSF14 8740 IFNB1 ALTERNATIVE PW Increased transcripts TREM1 54210 IFNB1 ALTERNATIVE PW Increased transcripts TREML4 285852 IFNB1 ALTERNATIVE PW Increased transcripts TRIM13 10206 IFNB1 ALTERNATIVE PW Increased transcripts TRMT61A 115708 IFNB1 ALTERNATIVE PW Increased transcripts TXNRD1 7296 IFNB1 ALTERNATIVE PW Increased transcripts URB2 9816 IFNB1 ALTERNATIVE PW Increased transcripts ZNF503 84858 IFNB1 ALTERNATIVE PW Increased transcripts ACLY 47 IFNB1 Signature ACSL1 2180 IFNB1 Signature ADAM19 8728 IFNB1 Signature ADAP2 55803 IFNB1 Signature ADAR 103 IFNB1 Signature ADGRE2 30817 IFNB1 Signature ADM 133 IFNB1 Signature AFF3 3899 IFNB1 Signature AGT 183 IFNB1 Signature AIM2 9447 IFNB1 Signature AKAP10 11216 IFNB1 Signature AKAP2 11217 IFNB1 Signature ALOX12 239 IFNB1 Signature ALOX5 240 IFNB1 Signature ANXA4 307 IFNB1 Signature APOBEC3B 9582 IFNB1 Signature APOBEC3G 60489 IFNB1 Signature APOL3 80833 IFNB1 Signature ATF3 467 IFNB1 Signature ATF5 22809 IFNB1 Signature ATM 472 IFNB1 Signature ATP13A1 57130 IFNB1 Signature B4GAT1 11041 IFNB1 Signature BAG1 573 IFNB1 Signature BAK1 578 IFNB1 Signature BARD1 580 IFNB1 Signature BCL11A 53335 IFNB1 Signature BCL7B 9275 IFNB1 Signature BGN 633 IFNB1 Signature BLNK 29760 IFNB1 Signature BLVRA 644 IFNB1 Signature BLZF1 8548 IFNB1 Signature BRCA1 672 IFNB1 Signature BRCA2 675 IFNB1 Signature BST2 684 IFNB1 Signature BUB1 699 IFNB1 Signature C3AR1 719 IFNB1 Signature CACNA1A 773 IFNB1 Signature CAD 790 IFNB1 Signature CALD1 800 IFNB1 Signature CAMK2A 815 IFNB1 Signature CAPN2 824 IFNB1 Signature CASP1 834 IFNB1 Signature CASP10 843 IFNB1 Signature CASP5 838 IFNB1 Signature CBR1 873 IFNB1 Signature CBWD1 55871 IFNB1 Signature CCL13 6357 IFNB1 Signature CCL3L1 6349 IFNB1 Signature CCL4 6351 IFNB1 Signature CCL7 6354 IFNB1 Signature CCL8 6355 IFNB1 Signature CCNA1 8900 IFNB1 Signature CCND2 894 IFNB1 Signature CCR1 1230 IFNB1 Signature CCR5 1234 IFNB1 Signature CCRL2 9034 IFNB1 Signature CD163 9332 IFNB1 Signature CD164 8763 IFNB1 Signature CD2AP 23607 IFNB1 Signature CD38 952 IFNB1 Signature CD4 920 IFNB1 Signature CD59 966 IFNB1 Signature CD69 969 IFNB1 Signature CD72 971 IFNB1 Signature CD86 942 IFNB1 Signature CDK17 5128 IFNB1 Signature CDKN1A 1026 IFNB1 Signature CENPA 1058 IFNB1 Signature CENPE 1062 IFNB1 Signature CFB 629 IFNB1 Signature CFLAR 8837 IFNB1 Signature CH25H 9023 IFNB1 Signature CHI3L2 1117 IFNB1 Signature CHKA 1119 IFNB1 Signature CISH 1154 IFNB1 Signature CKB 1152 IFNB1 Signature CMAHP 8418 IFNB1 Signature CNTN6 27255 IFNB1 Signature CNTRL 11064 IFNB1 Signature COL3A1 1281 IFNB1 Signature COX17 10063 IFNB1 Signature CSF2RB 1439 IFNB1 Signature CTSL 1514 IFNB1 Signature CXCL10 3627 IFNB1 Signature CXCL11 6373 IFNB1 Signature CXCL2 2920 IFNB1 Signature CXCL9 4283 IFNB1 Signature CXCR2 3579 IFNB1 Signature CYBB 1536 IFNB1 Signature CYP19A1 1588 IFNB1 Signature CYP2J2 1573 IFNB1 Signature DAB2 1601 IFNB1 Signature DEFA1 1667 IFNB1 Signature DEFB1 1672 IFNB1 Signature DHFR 1719 IFNB1 Signature DLL1 28514 IFNB1 Signature DMXL1 1657 IFNB1 Signature DNMT1 1786 IFNB1 Signature DRAP1 10589 IFNB1 Signature DSC2 1824 IFNB1 Signature DUSP5 1847 IFNB1 Signature DUSP7 1849 IFNB1 Signature DYNLT1 6993 IFNB1 Signature DYSF 8291 IFNB1 Signature E2F1 1869 IFNB1 Signature ECE1 1889 IFNB1 Signature EDN1 1906 IFNB1 Signature EGR1 1958 IFNB1 Signature EIF2AK2 5610 IFNB1 Signature EIF2B1 1967 IFNB1 Signature EIF4ENIF1 56478 IFNB1 Signature ELF1 1997 IFNB1 Signature ELF4 2000 IFNB1 Signature ENPP2 5168 IFNB1 Signature EPB41 2035 IFNB1 Signature ETV4 2118 IFNB1 Signature ETV6 2120 IFNB1 Signature F8 2157 IFNB1 Signature FAF1 11124 IFNB1 Signature FAS 355 IFNB1 Signature FBXW2 26190 IFNB1 Signature FCGR1A 2209 IFNB1 Signature FCMR 9214 IFNB1 Signature FGF1 2246 IFNB1 Signature FLNA 2316 IFNB1 Signature FMR1 2332 IFNB1 Signature FOXO1 2308 IFNB1 Signature FPR2 2358 IFNB1 Signature FTL 2512 IFNB1 Signature FUT4 2526 IFNB1 Signature GADD45B 4616 IFNB1 Signature GBAP1 2630 IFNB1 Signature GBP1 2633 IFNB1 Signature GBP2 2634 IFNB1 Signature GCH1 2643 IFNB1 Signature GCNT1 2650 IFNB1 Signature GLS 2744 IFNB1 Signature GMPR 2766 IFNB1 Signature GPI 2821 IFNB1 Signature GPR161 23432 IFNB1 Signature GUK1 2987 IFNB1 Signature HBG2 3048 IFNB1 Signature HCAR3 8843 IFNB1 Signature HHEX 3087 IFNB1 Signature HIST2H2AA3 8337 IFNB1 Signature HK2 3099 IFNB1 Signature HLA-DOA 3111 IFNB1 Signature HS6ST1 9394 IFNB1 Signature HSP90AA1 3320 IFNB1 Signature HSPA1A 3303 IFNB1 Signature HSPA1L 3305 IFNB1 Signature IDO1 3620 IFNB1 Signature IFI16 3428 IFNB1 Signature IFI27 3429 IFNB1 Signature IFI35 3430 IFNB1 Signature IFI44 10561 IFNB1 Signature IFI6 2537 IFNB1 Signature IFIT1 3434 IFNB1 Signature IFIT5 24138 IFNB1 Signature IFITM1 8519 IFNB1 Signature IFITM2 10581 IFNB1 Signature IFITM3 10410 IFNB1 Signature IFNG 3458 IFNB1 Signature IFRD1 3475 IFNB1 Signature IGL 3535 IFNB1 Signature IKBKE 9641 IFNB1 Signature IKBKG 8517 IFNB1 Signature IL15 3600 IFNB1 Signature IL15RA 3601 IFNB1 Signature IL18BP 10068 IFNB1 Signature IL18R1 8809 IFNB1 Signature IL1RN 3557 IFNB1 Signature IL6 3569 IFNB1 Signature IL7 3574 IFNB1 Signature INPP5D 3635 IFNB1 Signature INPPL1 3636 IFNB1 Signature IRF1 3659 IFNB1 Signature IRF2 3660 IFNB1 Signature IRF4 3662 IFNB1 Signature IRF7 3665 IFNB1 Signature IRF9 10379 IFNB1 Signature ISG15 9636 IFNB1 Signature ISG20 3669 IFNB1 Signature ITGAL 3683 IFNB1 Signature ITGAX 3687 IFNB1 Signature JAK2 3717 IFNB1 Signature JCHAIN 3512 IFNB1 Signature JUP 3728 IFNB1 Signature KCNA3 3738 IFNB1 Signature KCNMB1 3779 IFNB1 Signature KDELR2 11014 IFNB1 Signature KIF20B 9585 IFNB1 Signature KLF2 10365 IFNB1 Signature KLF6 1316 IFNB1 Signature KLRB1 3820 IFNB1 Signature KPNB1 3837 IFNB1 Signature KRT8 3856 IFNB1 Signature LAG3 3902 IFNB1 Signature LAMP3 27074 IFNB1 Signature LANCL1 10314 IFNB1 Signature LAP3 51056 IFNB1 Signature LBR 3930 IFNB1 Signature LEPR 3953 IFNB1 Signature LGALS2 3957 IFNB1 Signature LGALS3BP 3959 IFNB1 Signature LGALS9 3965 IFNB1 Signature LGMN 5641 IFNB1 Signature LILRA1 11024 IFNB1 Signature LINC00597 81698 IFNB1 Signature LMNB1 4001 IFNB1 Signature LMO2 4005 IFNB1 Signature LTA 4049 IFNB1 Signature LTB4R 1241 IFNB1 Signature LY6E 4061 IFNB1 Signature LYN 4067 IFNB1 Signature MAP2K5 5607 IFNB1 Signature MAP3K8 1326 IFNB1 Signature MARCKS 4082 IFNB1 Signature MBNL 4154 IFNB1 Signature MCL1 4170 IFNB1 Signature MED1 5469 IFNB1 Signature MEF2A 4205 IFNB1 Signature MFHAS1 9258 IFNB1 Signature MGLL 11343 IFNB1 Signature MNDA 4332 IFNB1 Signature MRPS15 64960 IFNB1 Signature MS4A7 58475 IFNB1 Signature MSR1 4481 IFNB1 Signature MX1 4599 IFNB1 Signature MX2 4600 IFNB1 Signature MYD88 4615 IFNB1 Signature NAMPT 10135 IFNB1 Signature NAPSA 9476 IFNB1 Signature NBN 4683 IFNB1 Signature NCF1 653361 IFNB1 Signature NCOA2 10499 IFNB1 Signature NEBL 10529 IFNB1 Signature NEK4 6787 IFNB1 Signature NFE2L3 9603 IFNB1 Signature NKTR 4820 IFNB1 Signature NMI 9111 IFNB1 Signature NOTCH1 4851 IFNB1 Signature NR3C1 2908 IFNB1 Signature NR4A3 8013 IFNB1 Signature NUB1 51667 IFNB1 Signature NUPR1 26471 IFNB1 Signature OAS1 4938 IFNB1 Signature OAS2 4939 IFNB1 Signature OAS3 4940 IFNB1 Signature PATJ 10207 IFNB1 Signature PAX5 5079 IFNB1 Signature PAX8 7849 IFNB1 Signature PDE4B 5142 IFNB1 Signature PDGFB 5155 IFNB1 Signature PDGFRL 5157 IFNB1 Signature PFKFB3 5209 IFNB1 Signature PFKP 5214 IFNB1 Signature PIM2 11040 IFNB1 Signature PKD2 5311 IFNB1 Signature PLEK 5341 IFNB1 Signature PLSCR1 5359 IFNB1 Signature PMAIP1 5366 IFNB1 Signature PML 5371 IFNB1 Signature PMS2 5395 IFNB1 Signature PPP2R2A 5520 IFNB1 Signature PRKAG1 5571 IFNB1 Signature PRKRA 8575 IFNB1 Signature PRKX 5613 IFNB1 Signature PSMB8 5696 IFNB1 Signature PSMB9 5698 IFNB1 Signature PTCH1 5727 IFNB1 Signature PTGER2 5732 IFNB1 Signature RALB 5899 IFNB1 Signature RASGRP1 10125 IFNB1 Signature RBBP6 5930 IFNB1 Signature RBCK1 10616 IFNB1 Signature RERE 473 IFNB1 Signature RGS1 5996 IFNB1 Signature RGS6 9628 IFNB1 Signature RIN1 9610 IFNB1 Signature RIPK1 8737 IFNB1 Signature RIPK3 11035 IFNB1 Signature RIPOR2 9750 IFNB1 Signature RNF114 55905 IFNB1 Signature RPS6KA5 9252 IFNB1 Signature RPS9 6203 IFNB1 Signature RRBP1 6238 IFNB1 Signature RTP4 64108 IFNB1 Signature SAT1 6303 IFNB1 Signature SCARB2 950 IFNB1 Signature SDS 10993 IFNB1 Signature SELL 6402 IFNB1 Signature SERPIND1 3053 IFNB1 Signature SERPING1 710 IFNB1 Signature SFTPB 6439 IFNB1 Signature SIDT2 51092 IFNB1 Signature SIT1 27240 IFNB1 Signature SLAMF1 6504 IFNB1 Signature SMO 6608 IFNB1 Signature SNX2 6643 IFNB1 Signature SOCS1 8651 IFNB1 Signature SOS1 6654 IFNB1 Signature SP100 6672 IFNB1 Signature SP110 3431 IFNB1 Signature SP140 11262 IFNB1 Signature SPIB 6689 IFNB1 Signature SPTA1 6708 IFNB1 Signature SPTLC2 9517 IFNB1 Signature SRRM2 23524 IFNB1 Signature SSB 6741 IFNB1 Signature ST3GAL5 8869 IFNB1 Signature STAP1 26228 IFNB1 Signature STAT1 6772 IFNB1 Signature STAT2 6773 IFNB1 Signature STOML2 30968 IFNB1 Signature STX11 8676 IFNB1 Signature SUPT3H 8464 IFNB1 Signature TANK 10010 IFNB1 Signature TAP1 6890 IFNB1 Signature TAP2 6891 IFNB1 Signature TAPBP 6892 IFNB1 Signature TARBP1 6894 IFNB1 Signature TBX21 30009 IFNB1 Signature TCN2 6948 IFNB1 Signature TFDP2 7029 IFNB1 Signature TFF1 7031 IFNB1 Signature TGM1 7051 IFNB1 Signature THY1 7070 IFNB1 Signature TLR1 7096 IFNB1 Signature TLR3 7098 IFNB1 Signature TLR7 51284 IFNB1 Signature TNFAIP2 7127 IFNB1 Signature TNFRSF11A 8792 IFNB1 Signature TNFSF10 8743 IFNB1 Signature TNFSF6 356 IFNB1 Signature TNK2 10188 IFNB1 Signature TOR1B 27348 IFNB1 Signature TRA2B 6434 IFNB1 Signature TRD 6964 IFNB1 Signature TRG 6965 IFNB1 Signature TRIM21 6737 IFNB1 Signature TRIM22 10346 IFNB1 Signature TRIM26 7726 IFNB1 Signature TRIM34 53840 IFNB1 Signature TRIM38 10475 IFNB1 Signature TSPAN15 23555 IFNB1 Signature TXK 7294 IFNB1 Signature UBA7 7318 IFNB1 Signature UBE2L6 9246 IFNB1 Signature UBE2S 27338 IFNB1 Signature UBE3A 7337 IFNB1 Signature UBQLN2 29978 IFNB1 Signature UNC93B1 81622 IFNB1 Signature USP15 9958 IFNB1 Signature USP18 11274 IFNB1 Signature USP25 29761 IFNB1 Signature USPL1 10208 IFNB1 Signature UVRAG 7405 IFNB1 Signature VAMP5 10791 IFNB1 Signature WARS 7453 IFNB1 Signature WIPF1 7456 IFNB1 Signature WT1 7490 IFNB1 Signature XAF1 54739 IFNB1 Signature ZNF107 51427 IFNB1 Signature ACLY 47 IFNG Signature ACSL1 2180 IFNG Signature AFF2 2334 IFNG Signature AIM2 9447 IFNG Signature AKAP10 11216 IFNG Signature APOL3 80833 IFNG Signature ATF3 467 IFNG Signature ATM 472 IFNG Signature C1QB 713 IFNG Signature C4A 720 IFNG Signature CALD1 800 IFNG Signature CASP1 834 IFNG Signature CASP10 843 IFNG Signature CCL8 6355 IFNG Signature CCND2 894 IFNG Signature CCR5 1234 IFNG Signature CD38 952 IFNG Signature CDKN1A 1026 IFNG Signature CFB 629 IFNG Signature CKB 1152 IFNG Signature CLEC10A 10462 IFNG Signature CPT1B 1375 IFNG Signature CSF2RB 1439 IFNG Signature CTNND2 1501 IFNG Signature CXCL10 3627 IFNG Signature CXCL11 6373 IFNG Signature CXCL9 4283 IFNG Signature CYBB 1536 IFNG Signature EDN1 1906 IFNG Signature EPB41 2035 IFNG Signature ETAA1 54465 IFNG Signature ETV4 2118 IFNG Signature F8 2157 IFNG Signature FAS 355 IFNG Signature FBLN1 2192 IFNG Signature FBXL2 25827 IFNG Signature FCGR1A 2209 IFNG Signature FLII 2314 IFNG Signature GADD45B 4616 IFNG Signature GBP1 2633 IFNG Signature GBP2 2634 IFNG Signature GCH1 2643 IFNG Signature GCNT1 2650 IFNG Signature GLS 2744 IFNG Signature GSTM5 2949 IFNG Signature HBG2 3048 IFNG Signature HHEX 3087 IFNG Signature HP 3240 IFNG Signature ICAM1 3383 IFNG Signature IDO1 3620 IFNG Signature IFI27 3429 IFNG Signature IFI44 10561 IFNG Signature IL15 3600 IFNG Signature IL15RA 3601 IFNG Signature IL18BP 10068 IFNG Signature IL1A 3552 IFNG Signature IL7 3574 IFNG Signature IRF1 3659 IFNG Signature IRF8 3394 IFNG Signature JAK2 3717 IFNG Signature JCHAIN 3512 IFNG Signature KLF2 10365 IFNG Signature LAP3 51056 IFNG Signature LIMK2 3985 IFNG Signature LMNB1 4001 IFNG Signature MMP25 64386 IFNG Signature MRPS15 64960 IFNG Signature MSR1 4481 IFNG Signature NET1 10276 IFNG Signature NIN 51199 IFNG Signature NKTR 4820 IFNG Signature NLRP1 22861 IFNG Signature NR3C1 2908 IFNG Signature OAS1 4938 IFNG Signature OAS3 4940 IFNG Signature P2RY13 53829 IFNG Signature PCDH9 5101 IFNG Signature PLA2G4C 8605 IFNG Signature PLEK 5341 IFNG Signature POLR2B 5431 IFNG Signature PSMB9 5698 IFNG Signature PTCH1 5727 IFNG Signature RALB 5899 IFNG Signature RGS1 5996 IFNG Signature SERPIND1 3053 IFNG Signature SERPING1 710 IFNG Signature SFTPB 6439 IFNG Signature SLAMF1 6504 IFNG Signature SLC1A5 6510 IFNG Signature SOCS1 8651 IFNG Signature SP100 6672 IFNG Signature SPRY4 81848 IFNG Signature SRRM2 23524 IFNG Signature STAT1 6772 IFNG Signature STAT2 6773 IFNG Signature STX11 8676 IFNG Signature TAP1 6890 IFNG Signature TAP2 6891 IFNG Signature TBX21 30009 IFNG Signature TENM1 10178 IFNG Signature TFF1 7031 IFNG Signature TNFAIP2 7127 IFNG Signature TNFSF10 8743 IFNG Signature UBD 10537 IFNG Signature UBE2C 11065 IFNG Signature UBE2L6 9246 IFNG Signature UBE3A 7337 IFNG Signature VAMP5 10791 IFNG Signature VSNL1 7447 IFNG Signature WARS 7453 IFNG Signature XRN1 54464 IFNG Signature ABCB10 23456 IFNW1 Signature ACLY 47 IFNW1 Signature ACSL1 2180 IFNW1 Signature ADAR 103 IFNW1 Signature ADM 133 IFNW1 Signature AGT 183 IFNW1 Signature AIM2 9447 IFNW1 Signature AKAP10 11216 IFNW1 Signature AKAP2 11217 IFNW1 Signature ALOX12 239 IFNW1 Signature ANXA4 307 IFNW1 Signature APOBEC3B 9582 IFNW1 Signature APOBEC3G 60489 IFNW1 Signature APOL3 80833 IFNW1 Signature ATF3 467 IFNW1 Signature ATF5 22809 IFNW1 Signature ATM 472 IFNW1 Signature B4GAT1 11041 IFNW1 Signature BAG1 573 IFNW1 Signature BARD1 580 IFNW1 Signature BCL11A 53335 IFNW1 Signature BCL7B 9275 IFNW1 Signature BLVRA 644 IFNW1 Signature BLZF1 8548 IFNW1 Signature BRCA1 672 IFNW1 Signature BRCA2 675 IFNW1 Signature BRD4 23476 IFNW1 Signature BST2 684 IFNW1 Signature C3AR1 719 IFNW1 Signature CAD 790 IFNW1 Signature CALD1 800 IFNW1 Signature CAMK2A 815 IFNW1 Signature CAPN2 824 IFNW1 Signature CASK 8573 IFNW1 Signature CASP1 834 IFNW1 Signature CASP10 843 IFNW1 Signature CASP5 838 IFNW1 Signature CBR1 873 IFNW1 Signature CBWD1 55871 IFNW1 Signature CCL13 6357 IFNW1 Signature CCL3L1 6349 IFNW1 Signature CCL7 6354 IFNW1 Signature CCL8 6355 IFNW1 Signature CCNA1 8900 IFNW1 Signature CCND2 894 IFNW1 Signature CCR1 1230 IFNW1 Signature CCR5 1234 IFNW1 Signature CCR7 1236 IFNW1 Signature CCRL2 9034 IFNW1 Signature CD164 8763 IFNW1 Signature CD2AP 23607 IFNW1 Signature CD38 952 IFNW1 Signature CD4 920 IFNW1 Signature CD47 961 IFNW1 Signature CD59 966 IFNW1 Signature CD69 969 IFNW1 Signature CDKN1A 1026 IFNW1 Signature CENPE 1062 IFNW1 Signature CFB 629 IFNW1 Signature CFLAR 8837 IFNW1 Signature CHKA 1119 IFNW1 Signature CKB 1152 IFNW1 Signature CMAHP 8418 IFNW1 Signature CNTN6 27255 IFNW1 Signature CNTRL 11064 IFNW1 Signature COL3A1 1281 IFNW1 Signature CSF2RB 1439 IFNW1 Signature CTSL 1514 IFNW1 Signature CXCL10 3627 IFNW1 Signature CXCL11 6373 IFNW1 Signature CXCL9 4283 IFNW1 Signature CXCR2 3579 IFNW1 Signature CYBB 1536 IFNW1 Signature CYP19A1 1588 IFNW1 Signature CYP2J2 1573 IFNW1 Signature DEFB1 1672 IFNW1 Signature DLL1 28514 IFNW1 Signature DSC2 1824 IFNW1 Signature DUSP5 1847 IFNW1 Signature DUSP7 1849 IFNW1 Signature DYNLT1 6993 IFNW1 Signature DYSF 8291 IFNW1 Signature E2F1 1869 IFNW1 Signature ECE1 1889 IFNW1 Signature EDN1 1906 IFNW1 Signature EGR1 1958 IFNW1 Signature EIF2AK2 5610 IFNW1 Signature EIF2B1 1967 IFNW1 Signature EIF4ENIF1 56478 IFNW1 Signature ENPP2 5168 IFNW1 Signature EPB41 2035 IFNW1 Signature ERCC4 2072 IFNW1 Signature ETV4 2118 IFNW1 Signature ETV6 2120 IFNW1 Signature F8 2157 IFNW1 Signature FAF1 11124 IFNW1 Signature FAS 355 IFNW1 Signature FCER1G 2207 IFNW1 Signature FGF1 2246 IFNW1 Signature FGF13 2258 IFNW1 Signature FGL2 10875 IFNW1 Signature FLNA 2316 IFNW1 Signature FMR1 2332 IFNW1 Signature FOXO1 2308 IFNW1 Signature FTL 2512 IFNW1 Signature FUT4 2526 IFNW1 Signature GADD45B 4616 IFNW1 Signature GBAP1 2630 IFNW1 Signature GBP1 2633 IFNW1 Signature GBP2 2634 IFNW1 Signature GCH1 2643 IFNW1 Signature GCNT1 2650 IFNW1 Signature GLB1 2720 IFNW1 Signature GLS 2744 IFNW1 Signature GMPR 2766 IFNW1 Signature GPR161 23432 IFNW1 Signature GSTM5 2949 IFNW1 Signature GUK1 2987 IFNW1 Signature HBG2 3048 IFNW1 Signature HHEX 3087 IFNW1 Signature HIST2H2AA3 8337 IFNW1 Signature HLA-DOA 3111 IFNW1 Signature HS6ST1 9394 IFNW1 Signature HSP90AA1 3320 IFNW1 Signature HSPA1A 3303 IFNW1 Signature IDO1 3620 IFNW1 Signature IFI16 3428 IFNW1 Signature IFI27 3429 IFNW1 Signature IFI35 3430 IFNW1 Signature IFI44 10561 IFNW1 Signature IFI6 2537 IFNW1 Signature IFIT1 3434 IFNW1 Signature IFIT5 24138 IFNW1 Signature IFITM1 8519 IFNW1 Signature IFITM2 10581 IFNW1 Signature IFITM3 10410 IFNW1 Signature IFRD1 3475 IFNW1 Signature IGL 3535 IFNW1 Signature IKBKG 8517 IFNW1 Signature IL15 3600 IFNW1 Signature IL15RA 3601 IFNW1 Signature IL18R1 8809 IFNW1 Signature IL1RN 3557 IFNW1 Signature IL6 3569 IFNW1 Signature IL7 3574 IFNW1 Signature INPPL1 3636 IFNW1 Signature IRF1 3659 IFNW1 Signature IRF2 3660 IFNW1 Signature IRF7 3665 IFNW1 Signature IRF8 3394 IFNW1 Signature ISG15 9636 IFNW1 Signature ISG20 3669 IFNW1 Signature ITIH2 3698 IFNW1 Signature JAK2 3717 IFNW1 Signature JCHAIN 3512 IFNW1 Signature JUP 3728 IFNW1 Signature KCNA3 3738 IFNW1 Signature KDELR2 11014 IFNW1 Signature KIF20B 9585 IFNW1 Signature KLF6 1316 IFNW1 Signature KPNB1 3837 IFNW1 Signature KRT8 3856 IFNW1 Signature LAG3 3902 IFNW1 Signature LAMP3 27074 IFNW1 Signature LAP3 51056 IFNW1 Signature LEPR 3953 IFNW1 Signature LGALS2 3957 IFNW1 Signature LGALS3BP 3959 IFNW1 Signature LGALS9 3965 IFNW1 Signature LGMN 5641 IFNW1 Signature LINC00597 81698 IFNW1 Signature LMNB1 4001 IFNW1 Signature LMO2 4005 IFNW1 Signature LY6E 4061 IFNW1 Signature LYN 4067 IFNW1 Signature MAP2K5 5607 IFNW1 Signature MARCKS 4082 IFNW1 Signature MBNL1 4154 IFNW1 Signature MCL1 4170 IFNW1 Signature MED1 5469 IFNW1 Signature MEF2A 4205 IFNW1 Signature MGLL 11343 IFNW1 Signature MLF1 4291 IFNW1 Signature MMP16 4325 IFNW1 Signature MNDA 4332 IFNW1 Signature MRPS15 64960 IFNW1 Signature MS4A7 58475 IFNW1 Signature MSR1 4481 IFNW1 Signature MX1 4599 IFNW1 Signature MX2 4600 IFNW1 Signature MYD88 4615 IFNW1 Signature NAMPT 10135 IFNW1 Signature NCF1 653361 IFNW1 Signature NFE2L3 9603 IFNW1 Signature NKTR 4820 IFNW1 Signature NMI 9111 IFNW1 Signature NPTX1 4884 IFNW1 Signature NR3C1 2908 IFNW1 Signature NUB1 51667 IFNW1 Signature NUPR1 26471 IFNW1 Signature OAS1 4938 IFNW1 Signature OAS2 4939 IFNW1 Signature OAS3 4940 IFNW1 Signature OSBPL1A 114876 IFNW1 Signature PATJ 10207 IFNW1 Signature PAX8 7849 IFNW1 Signature PDGFB 5155 IFNW1 Signature PDGFRL 5157 IFNW1 Signature PKD2 5311 IFNW1 Signature PLEK 5341 IFNW1 Signature PLSCR1 5359 IFNW1 Signature PMAIP1 5366 IFNW1 Signature PML 5371 IFNW1 Signature PPP2R2A 5520 IFNW1 Signature PRKAG1 5571 IFNW1 Signature PRKRA 8575 IFNW1 Signature PSMB9 5698 IFNW1 Signature PTCH1 5727 IFNW1 Signature PTGER2 5732 IFNW1 Signature RALB 5899 IFNW1 Signature RBBP6 5930 IFNW1 Signature RBCK1 10616 IFNW1 Signature RERE 473 IFNW1 Signature RGS1 5996 IFNW1 Signature RGS6 9628 IFNW1 Signature RPS6KA5 9252 IFNW1 Signature RTP4 64108 IFNW1 Signature SAT1 6303 IFNW1 Signature SCARB2 950 IFNW1 Signature SDS 10993 IFNW1 Signature SELL 6402 IFNW1 Signature SERPIND1 3053 IFNW1 Signature SERPING1 710 IFNW1 Signature SFT2D2 375035 IFNW1 Signature SIT1 27240 IFNW1 Signature SLC30A4 7782 IFNW1 Signature SOCS1 8651 IFNW1 Signature SOS1 6654 IFNW1 Signature SP100 6672 IFNW1 Signature SP110 3431 IFNW1 Signature SP140 11262 IFNW1 Signature SPIB 6689 IFNW1 Signature SRRM2 23524 IFNW1 Signature ST3GAL5 8869 IFNW1 Signature STAP1 26228 IFNW1 Signature STAT1 6772 IFNW1 Signature STAT2 6773 IFNW1 Signature STX11 8676 IFNW1 Signature SUPT3H 8464 IFNW1 Signature TAP1 6890 IFNW1 Signature TAP2 6891 IFNW1 Signature TARBP1 6894 IFNW1 Signature TBX21 30009 IFNW1 Signature TCN2 6948 IFNW1 Signature TFDP2 7029 IFNW1 Signature TFF1 7031 IFNW1 Signature TGM1 7051 IFNW1 Signature THY1 7070 IFNW1 Signature TLR3 7098 IFNW1 Signature TLR7 51284 IFNW1 Signature TNFAIP3 7128 IFNW1 Signature TNFRSF11A 8792 IFNW1 Signature TNFSF10 8743 IFNW1 Signature TNFSF6 356 IFNW1 Signature TNK2 10188 IFNW1 Signature TOR1B 27348 IFNW1 Signature TRA2B 6434 IFNW1 Signature TRD 6964 IFNW1 Signature TRIM21 6737 IFNW1 Signature TRIM22 10346 IFNW1 Signature TRIM34 53840 IFNW1 Signature TRIM38 10475 IFNW1 Signature UBA7 7318 IFNW1 Signature UBE2C 11065 IFNW1 Signature UBE2L6 9246 IFNW1 Signature UBE2S 27338 IFNW1 Signature UNC93B1 81622 IFNW1 Signature USP18 11274 IFNW1 Signature USP25 29761 IFNW1 Signature WARS 7453 IFNW1 Signature WIPF1 7456 IFNW1 Signature WT1 7490 IFNW1 Signature XAF1 54739 IFNW1 Signature ZNF107 51427 IFNW1 Signature ACSL1 2180 TYPE I and TYPE II IFN Core AIM2 9447 TYPE I and TYPE II IFN Core APOL3 80833 TYPE I and TYPE II IFN Core ATF3 467 TYPE I and TYPE II IFN Core CASP1 834 TYPE I and TYPE II IFN Core CASP10 843 TYPE I and TYPE II IFN Core CCL8 6355 TYPE I and TYPE II IFN Core CCND2 894 TYPE I and TYPE II IFN Core CD38 952 TYPE I and TYPE II IFN Core CDKN1A 1026 TYPE I and TYPE II IFN Core CFB 629 TYPE I and TYPE II IFN Core CXCL10 3627 TYPE I and TYPE II IFN Core CXCL11 6373 TYPE I and TYPE II IFN Core CXCL9 4283 TYPE I and TYPE II IFN Core EDN1 1906 TYPE I and TYPE II IFN Core EPB41 2035 TYPE I and TYPE II IFN Core ETV4 2118 TYPE I and TYPE II IFN Core F8 2157 TYPE I and TYPE II IFN Core FAS 355 TYPE I and TYPE II IFN Core GADD45B 4616 TYPE I and TYPE II IFN Core GBP1 2633 TYPE I and TYPE II IFN Core GBP2 2634 TYPE I and TYPE II IFN Core GCH1 2643 TYPE I and TYPE II IFN Core GCNT1 2650 TYPE I and TYPE II IFN Core GLS 2744 TYPE I and TYPE II IFN Core HBG2 3048 TYPE I and TYPE II IFN Core IDO1 3620 TYPE I and TYPE II IFN Core IFI27 3429 TYPE I and TYPE II IFN Core IFI44 10561 TYPE I and TYPE II IFN Core IL15 3600 TYPE I and TYPE II IFN Core IL15RA 3601 TYPE I and TYPE II IFN Core JAK2 3717 TYPE I and TYPE II IFN Core LAP3 51056 TYPE I and TYPE II IFN Core LMNB1 4001 TYPE I and TYPE II IFN Core MRPS15 64960 TYPE I and TYPE II IFN Core MSR1 4481 TYPE I and TYPE II IFN Core NKTR 4820 TYPE I and TYPE II IFN Core NR3C1 2908 TYPE I and TYPE II IFN Core OAS1 4938 TYPE I and TYPE II IFN Core OAS3 4940 TYPE I and TYPE II IFN Core PSMB9 5698 TYPE I and TYPE II IFN Core PTCH1 5727 TYPE I and TYPE II IFN Core RGS1 5996 TYPE I and TYPE II IFN Core SERPING1 710 TYPE I and TYPE II IFN Core SOCS1 8651 TYPE I and TYPE II IFN Core SP100 6672 TYPE I and TYPE II IFN Core STAT1 6772 TYPE I and TYPE II IFN Core STAT2 6773 TYPE I and TYPE II IFN Core STX11 8676 TYPE I and TYPE II IFN Core TAP1 6890 TYPE I and TYPE II IFN Core TAP2 6891 TYPE I and TYPE II IFN Core TNFSF10 8743 TYPE I and TYPE II IFN Core UBE2L6 9246 TYPE I and TYPE II IFN Core WARS 7453 TYPE I and TYPE II IFN Core ACSL1 2180 Type I IFN Core Signature ADAR 103 Type I IFN Core Signature AGT 183 Type I IFN Core Signature AIM2 9447 Type I IFN Core Signature AKAP2 11217 Type I IFN Core Signature APOBEC3B 9582 Type I IFN Core Signature APOBEC3G 60489 Type I IFN Core Signature APOL3 80833 Type I IFN Core Signature ATF3 467 Type I IFN Core Signature ATF5 22809 Type I IFN Core Signature BAG1 573 Type I IFN Core Signature BARD1 580 Type I IFN Core Signature BCL7B 9275 Type I IFN Core Signature BLVRA 644 Type I IFN Core Signature BRCA1 672 Type I IFN Core Signature BRCA2 675 Type I IFN Core Signature BST2 684 Type I IFN Core Signature CAD 790 Type I IFN Core Signature CAMK2A 815 Type I IFN Core Signature CASP1 834 Type I IFN Core Signature CASP10 843 Type I IFN Core Signature CASP5 838 Type I IFN Core Signature CBR1 873 Type I IFN Core Signature CBWD1 55871 Type I IFN Core Signature CCL13 6357 Type I IFN Core Signature CCL7 6354 Type I IFN Core Signature CCL8 6355 Type I IFN Core Signature CCNA1 8900 Type I IFN Core Signature CCND2 894 Type I IFN Core Signature CD2AP 23607 Type I IFN Core Signature CD38 952 Type I IFN Core Signature CD4 920 Type I IFN Core Signature CD69 969 Type I IFN Core Signature CDKN1A 1026 Type I IFN Core Signature CFB 629 Type I IFN Core Signature CHKA 1119 Type I IFN Core Signature CNTN6 27255 Type I IFN Core Signature COL3A1 1281 Type I IFN Core Signature CTSL 1514 Type I IFN Core Signature CXCL10 3627 Type I IFN Core Signature CXCL11 6373 Type I IFN Core Signature CXCL9 4283 Type I IFN Core Signature CXCR2 3579 Type I IFN Core Signature CYP2J2 1573 Type I IFN Core Signature DEFB1 1672 Type I IFN Core Signature DLL1 28514 Type I IFN Core Signature DSC2 1824 Type I IFN Core Signature DUSP5 1847 Type I IFN Core Signature DUSP7 1849 Type I IFN Core Signature DYNLT1 6993 Type I IFN Core Signature DYSF 8291 Type I IFN Core Signature ECE1 1889 Type I IFN Core Signature EDN1 1906 Type I IFN Core Signature EIF2AK2 5610 Type I IFN Core Signature EIF2B1 1967 Type I IFN Core Signature EIF4ENIF1 56478 Type I IFN Core Signature ENPP2 5168 Type I IFN Core Signature EPB41 2035 Type I IFN Core Signature ETV4 2118 Type I IFN Core Signature F8 2157 Type I IFN Core Signature FAF1 11124 Type I IFN Core Signature FAS 355 Type I IFN Core Signature FASLG 356 Type I IFN Core Signature FGF1 2246 Type I IFN Core Signature FLNA 2316 Type I IFN Core Signature FOXO1 2308 Type I IFN Core Signature FTL 2512 Type I IFN Core Signature FUT4 2526 Type I IFN Core Signature GADD45B 4616 Type I IFN Core Signature GBAP1 2630 Type I IFN Core Signature GBP1 2633 Type I IFN Core Signature GBP2 2634 Type I IFN Core Signature GCH1 2643 Type I IFN Core Signature GCNT1 2650 Type I IFN Core Signature GLS 2744 Type I IFN Core Signature GMPR 2766 Type I IFN Core Signature GPR161 23432 Type I IFN Core Signature GUK1 2987 Type I IFN Core Signature HBG2 3048 Type I IFN Core Signature HIST2H2AA3 8337 Type I IFN Core Signature HLA-DOA 3111 Type I IFN Core Signature HS6ST1 9394 Type I IFN Core Signature HSP90AA1 3320 Type I IFN Core Signature IDO1 3620 Type I IFN Core Signature IFI16 3428 Type I IFN Core Signature IFI27 3429 Type I IFN Core Signature IFI35 3430 Type I IFN Core Signature IFI44 10561 Type I IFN Core Signature IFI6 2537 Type I IFN Core Signature IFIT1 3434 Type I IFN Core Signature IFIT5 24138 Type I IFN Core Signature IFITM1 8519 Type I IFN Core Signature IFITM2 10581 Type I IFN Core Signature IFITM3 10410 Type I IFN Core Signature IFRD1 3475 Type I IFN Core Signature IGL 3535 Type I IFN Core Signature IKBKG 8517 Type I IFN Core Signature IL15 3600 Type I IFN Core Signature IL15RA 3601 Type I IFN Core Signature IL1RN 3557 Type I IFN Core Signature IL6 3569 Type I IFN Core Signature INPPL1 3636 Type I IFN Core Signature IRF2 3660 Type I IFN Core Signature IRF7 3665 Type I IFN Core Signature ISG15 9636 Type I IFN Core Signature ISG20 3669 Type I IFN Core Signature JAK2 3717 Type I IFN Core Signature JUP 3728 Type I IFN Core Signature KCNA3 3738 Type I IFN Core Signature KDELR2 11014 Type I IFN Core Signature KIF20B 9585 Type I IFN Core Signature KLF6 1316 Type I IFN Core Signature KPNB1 3837 Type I IFN Core Signature KRT8 3856 Type I IFN Core Signature LAG3 3902 Type I IFN Core Signature LAMP3 27074 Type I IFN Core Signature LAP3 51056 Type I IFN Core Signature LEPR 3953 Type I IFN Core Signature LGALS2 3957 Type I IFN Core Signature LGALS3BP 3959 Type I IFN Core Signature LGALS9 3965 Type I IFN Core Signature LGMN 5641 Type I IFN Core Signature LMNB1 4001 Type I IFN Core Signature LMO2 4005 Type I IFN Core Signature LY6E 4061 Type I IFN Core Signature MAP2K5 5607 Type I IFN Core Signature MCL1 4170 Type I IFN Core Signature MED1 5469 Type I IFN Core Signature MGLL 11343 Type I IFN Core Signature MNDA 4332 Type I IFN Core Signature MRPS15 64960 Type I IFN Core Signature MSR1 4481 Type I IFN Core Signature MX1 4599 Type I IFN Core Signature MX2 4600 Type I IFN Core Signature MYD88 4615 Type I IFN Core Signature NAMPT 10135 Type I IFN Core Signature NFE2L3 9603 Type I IFN Core Signature NKTR 4820 Type I IFN Core Signature NMI 9111 Type I IFN Core Signature NR3C1 2908 Type I IFN Core Signature NUB1 51667 Type I IFN Core Signature NUPR1 26471 Type I IFN Core Signature OAS1 4938 Type I IFN Core Signature OAS2 4939 Type I IFN Core Signature OAS3 4940 Type I IFN Core Signature PATJ 10207 Type I IFN Core Signature PDGFB 5155 Type I IFN Core Signature PDGFRL 5157 Type I IFN Core Signature PKD2 5311 Type I IFN Core Signature PLSCR1 5359 Type I IFN Core Signature PMAIP1 5366 Type I IFN Core Signature PML 5371 Type I IFN Core Signature PRKRA 8575 Type I IFN Core Signature PSMB9 5698 Type I IFN Core Signature PTCH1 5727 Type I IFN Core Signature RBCK1 10616 Type I IFN Core Signature RGS1 5996 Type I IFN Core Signature RGS6 9628 Type I IFN Core Signature RTP4 64108 Type I IFN Core Signature SAT1 6303 Type I IFN Core Signature SCARB2 950 Type I IFN Core Signature SERPING1 710 Type I IFN Core Signature SIT1 27240 Type I IFN Core Signature SOCS1 8651 Type I IFN Core Signature SP100 6672 Type I IFN Core Signature SP110 3431 Type I IFN Core Signature SP140 11262 Type I IFN Core Signature SPIB 6689 Type I IFN Core Signature ST3GAL5 8869 Type I IFN Core Signature STAP1 26228 Type I IFN Core Signature STAT1 6772 Type I IFN Core Signature STAT2 6773 Type I IFN Core Signature STX11 8676 Type I IFN Core Signature SUPT3H 8464 Type I IFN Core Signature TAPI 6890 Type I IFN Core Signature TAP2 6891 Type I IFN Core Signature TARBP1 6894 Type I IFN Core Signature TCN2 6948 Type I IFN Core Signature TFDP2 7029 Type I IFN Core Signature TGM1 7051 Type I IFN Core Signature TLR3 7098 Type I IFN Core Signature TLR7 51284 Type I IFN Core Signature TNFRSF11A 8792 Type I IFN Core Signature TNFSF10 8743 Type I IFN Core Signature TNK2 10188 Type I IFN Core Signature TOR1B 27348 Type I IFN Core Signature TRA2B 6434 Type I IFN Core Signature TRD 6964 Type I IFN Core Signature TRIM21 6737 Type I IFN Core Signature TRIM22 10346 Type I IFN Core Signature TRIM34 53840 Type I IFN Core Signature TRIM38 10475 Type I IFN Core Signature UBA7 7318 Type I IFN Core Signature UBE2L6 9246 Type I IFN Core Signature UBE2S 27338 Type I IFN Core Signature UNC93B1 81622 Type I IFN Core Signature USP18 11274 Type I IFN Core Signature WARS 7453 Type I IFN Core Signature WT1 7490 Type I IFN Core Signature XAF1 54739 Type I IFN Core Signature

Table of UCSC Eils Lung Modified geneSymbol geneEntrezID GeneSet ABCA1 19 AT1_Cat ADIRF 10974 AT1_Cat AGER 177 AT1_Cat ANKRD29 147463 AT1_Cat AQP4 361 AT1_Cat ARAP2 116984 AT1_Cat ARHGEF26 26084 AT1_Cat ATF7IP2 80063 AT1_Cat CAV1 857 AT1_Cat CAV2 858 AT1_Cat CCDC85A 114800 AT1_Cat CLDN18 51208 AT1_Cat CLIC5 53405 AT1_Cat CNTN6 27255 AT1_Cat COL4A4 1286 AT1_Cat CYP4B1 1580 AT1_Cat CYR61 3491 AT1_Cat DAPK2 23604 AT1_Cat DOCK4 9732 AT1_Cat EMP2 2013 AT1_Cat EPB41L5 57669 AT1_Cat FAM189A2 9413 AT1_Cat GALNT13 114805 AT1_Cat GPC5 2262 AT1_Cat GPM6A 2823 AT1_Cat HOMER1 9456 AT1_Cat KAL1 3730 AT1_Cat KCNT2 343450 AT1_Cat KHDRBS2 202559 AT1_Cat KRT18 3875 AT1_Cat KRT19 3880 AT1_Cat KRT7 3855 AT1_Cat LAMA3 3909 AT1_Cat LIN7A 8825 AT1_Cat LINC00842 643650 AT1_Cat MAP2 4133 AT1_Cat MS4A15 219995 AT1_Cat MYO16 23026 AT1_Cat MYO16-AS1 100885782 AT1_Cat NEBL 10529 AT1_Cat NTM 50863 AT1_Cat PAPSS2 9060 AT1_Cat PHLDB2 90102 AT1_Cat PLCE1 51196 AT1_Cat PTPN21 11099 AT1_Cat RANBP17 64901 AT1_Cat RHOBTB3 22836 AT1_Cat ROR1 4919 AT1_Cat S100A10 6281 AT1_Cat SCD5 79966 AT1_Cat SCEL 8796 AT1_Cat SLC1A1 6505 AT1_Cat SLC39A8 64116 AT1_Cat SLC8A1-AS1 100128590 AT1_Cat SPOCK2 9806 AT1_Cat SRPX2 27286 AT1_Cat ST6GALNAC5 81849 AT1_Cat TNFRSF12A 51330 AT1_Cat TSPAN13 27075 AT1_Cat VEGFA 7422 AT1_Cat ABCA3 21 AT2_Cat ABCC9 10060 AT2_Cat ACOXL 55289 AT2_Cat AGBL1 123624 AT2_Cat AGR2 10551 AT2_Cat ALPL 249 AT2_Cat ARRDC3 57561 AT2_Cat C3 718 AT2_Cat C8orf34 116328 AT2_Cat C8orf4 56892 AT2_Cat CACHD1 57685 AT2_Cat CCDC141 285025 AT2_Cat COLEC12 81035 AT2_Cat CTSH 1512 AT2_Cat DLG2 1740 AT2_Cat DLGAP1 9229 AT2_Cat DMBT1 1755 AT2_Cat ETV1 2115 AT2_Cat ETV5 2119 AT2_Cat FAM155A 728215 AT2_Cat FLRT3 23767 AT2_Cat FNIP2 57600 AT2_Cat FREM2 341640 AT2_Cat HHIP 64399 AT2_Cat KCNJ15 3772 AT2_Cat KCNQ3 3786 AT2_Cat KIAA1324L 222223 AT2_Cat LEPREL1 55214 AT2_Cat LHFPL3 375612 AT2_Cat LINC01090 104355152 AT2_Cat LRP2BP 55805 AT2_Cat LRRK2 120892 AT2_Cat MACROD2 140733 AT2_Cat MAPK10 5602 AT2_Cat MFSD2A 84879 AT2_Cat NAPSA 9476 AT2_Cat NECAB1 64168 AT2_Cat NTN4 59277 AT2_Cat PARM1 25849 AT2_Cat PCDH9 5101 AT2_Cat PCDP1 200373 AT2_Cat PCYOX1 51449 AT2_Cat PGC 5225 AT2_Cat PTGFR 5737 AT2_Cat PTPN13 5783 AT2_Cat RASGRF1 5923 AT2_Cat RGS16 6004 AT2_Cat RND1 27289 AT2_Cat SCN1A 6323 AT2_Cat SDR16C5 195814 AT2_Cat SERPINA1 5265 AT2_Cat SFTPA2 729238 AT2_Cat SFTPC 6440 AT2_Cat SFTPD 6441 AT2_Cat TMEM163 81615 AT2_Cat TMEM164 84187 AT2_Cat TTN 7273 AT2_Cat WIF1 11197 AT2_Cat ZNF385B 151126 AT2_Cat ADGB 79747 Ciliated AGBL4 84871 Ciliated AK9 221264 Ciliated ANKFN1 162282 Ciliated AQP4-AS1 147429 Ciliated ARMC3 219681 Ciliated C12orf55 144535 Ciliated C20orf26 26074 Ciliated C20orf85 128602 Ciliated C21orf58 54058 Ciliated C4orf47 441054 Ciliated C9orf117 286207 Ciliated C9orf171 389799 Ciliated CAPS 828 Ciliated CCDC146 57639 Ciliated CCDC17 149483 Ciliated CCDC170 80129 Ciliated CCDC30 728621 Ciliated CCDC42B 387885 Ciliated CCDC78 124093 Ciliated CLEC19A 728276 Ciliated DCDC1 341019 Ciliated DNAAF1 123872 Ciliated DNAH11 8701 Ciliated DNAH12 201625 Ciliated DNAH3 55567 Ciliated DNAH6 1768 Ciliated DNAH7 56171 Ciliated DNAI2 64446 Ciliated DPPA2 151871 Ciliated DTHD1 401124 Ciliated DYNC2H1 79659 Ciliated ECT2L 345930 Ciliated ESRRG 2104 Ciliated FABP6 2172 Ciliated FAM154B 283726 Ciliated FHAD1 114827 Ciliated IFLTD1 160492 Ciliated KIAA0825 285600 Ciliated KIAA1377 57562 Ciliated LRGUK 136332 Ciliated LRRC48 83450 Ciliated MROH9 80133 Ciliated MS4A8 83661 Ciliated NEK10 152110 Ciliated NEK11 79858 Ciliated NELL2 4753 Ciliated PACRG 135138 Ciliated PRMT8 56341 Ciliated PTPRT 11122 Ciliated PTRH1 138428 Ciliated RP1 6101 Ciliated RSPH1 89765 Ciliated SLCO2B1 11309 Ciliated SPAG16 79582 Ciliated SPEF2 79925 Ciliated TEKT1 83659 Ciliated TMEM232 642987 Ciliated TPPP3 51673 Ciliated TSPAN19 144448 Ciliated TTC18 118491 Ciliated TTC29 83894 Ciliated ULK4 54986 Ciliated VWA3A 146177 Ciliated VWA3B 200403 Ciliated WDR78 79819 Ciliated WDR96 80217 Ciliated ZBBX 79740 Ciliated ZMYND10 51364 Ciliated AADAC 13 Club ADAM28 10863 Club AGR3 155465 Club BMP6 654 Club BPIFB1 92747 Club CASC15 401237 Club CFH 3075 Club CHST9 83539 Club CIT 11113 Club CLIC6 54102 Club CLU 1191 Club CNTN4 152330 Club CP 1356 Club CXCL2 2920 Club ERN2 10595 Club EYA2 2139 Club FAM129A 116496 Club FGFR2 2263 Club FMO2 2327 Club FOLR1 2348 Club FRAS1 80144 Club GDF15 9518 Club GLIS3 169792 Club HS3ST5 222537 Club KCNQ5 56479 Club KIAA1324 57535 Club KLK10 5655 Club KLK11 11012 Club KRT15 3866 Club LINC00511 400619 Club MAGI2 9863 Club MIR205HG 642587 Club MME 4311 Club MMP7 4316 Club MT-CO1 4512 Club MT-CO2 4513 Club MT-ND1 4535 Club MT-ND3 4537 Club MUC4 4585 Club NCEH1 57552 Club NHS 4810 Club NTN1 9423 Club PIGR 5284 Club PLCL1 5334 Club PRSS12 8492 Club SAA1 6288 Club SCGB1A1 7356 Club SOX4 6659 Club SRGAP3 9901 Club TP63 8626 Club VTCN1 79679 Club WFDC2 10406 Club AKT3 10000 Endothelial ANO2 57101 Endothelial AQP1 358 Endothelial BST2 684 Endothelial C10orf10 11067 Endothelial CA4 762 Endothelial CLDN5 7122 Endothelial CLEC14A 161198 Endothelial COL4A2 1284 Endothelial CTNNAL1 8727 Endothelial CYYR1 116159 Endothelial DARC 2532 Endothelial DPYSL3 1809 Endothelial ELTD1 64123 Endothelial EMP1 2012 Endothelial ENPP2 5168 Endothelial EXOC6 54536 Endothelial FLI1 2313 Endothelial FLT1 2321 Endothelial FOXO1 2308 Endothelial GNG11 2791 Endothelial HLA-E 3133 Endothelial ICAM2 3384 Endothelial IGFBP4 3487 Endothelial IL33 90865 Endothelial ITGA1 3672 Endothelial ITM2A 9452 Endothelial MEF2C 4208 Endothelial MEIS2 4212 Endothelial PALMD 54873 Endothelial PLCB1 23236 Endothelial PLCB4 5332 Endothelial PREX2 80243 Endothelial PRSS23 11098 Endothelial PTPRB 5787 Endothelial RAMP2 10266 Endothelial SEMA6A 57556 Endothelial SH3BP5 9467 Endothelial SLCO2A1 6578 Endothelial SOCS3 9021 Endothelial SPARC 6678 Endothelial TCF4 6925 Endothelial TGFBR3 7049 Endothelial THBD 7056 Endothelial TM4SF1 4071 Endothelial 3-Mar 115123 Lymphatic_Endothelium AKAP12 9590 Lymphatic_Endothelium CCL21 6366 Lymphatic_Endothelium CNKSR3 154043 Lymphatic_Endothelium CNTNAP3B 728577 Lymphatic_Endothelium COL8A1 1295 Lymphatic_Endothelium EPB41L3 23136 Lymphatic_Endothelium FABP4 2167 Lymphatic_Endothelium FLRT2 23768 Lymphatic_Endothelium FLT4 2324 Lymphatic_Endothelium GRAPL 400581 Lymphatic_Endothelium KALRN 8997 Lymphatic_Endothelium KCNIP4 80333 Lymphatic_Endothelium KLHL4 56062 Lymphatic_Endothelium NPAS3 64067 Lymphatic_Endothelium NRP2 8828 Lymphatic_Endothelium PDE1A 5136 Lymphatic_Endothelium PDE7B 27115 Lymphatic_Endothelium PKHD1L1 93035 Lymphatic_Endothelium PPFIBP1 8496 Lymphatic_Endothelium PROX1 5629 Lymphatic_Endothelium RELN 5649 Lymphatic_Endothelium RHOJ 57381 Lymphatic_Endothelium SEMA3D 223117 Lymphatic_Endothelium SMOC2 64094 Lymphatic_Endothelium SNTG2 54221 Lymphatic_Endothelium ST6GALNAC3 256435 Lymphatic_Endothelium STON2 85439 Lymphatic_Endothelium TFF3 7033 Lymphatic_Endothelium TFPI 7035 Lymphatic_Endothelium TSHZ2 128553 Lymphatic_Endothelium TSPAN5 10098 Lymphatic_Endothelium VAV3 10451 Lymphatic_Endothelium ZDHHC14 79683 Lymphatic_Endothelium ZNF521 25925 Lymphatic_Endothelium

Table of All Myeloid Populations geneSymbol EntrezID Category ANXA1 301 AQP1+ interstitial macrophages steady-state synovium AQP1 358 AQP1+ interstitial macrophages steady-state synovium CD9 928 AQP1+ interstitial macrophages steady-state synovium FXYD2 486 AQP1+ interstitial macrophages steady-state synovium LYVE1 10894 AQP1+ interstitial macrophages steady-state synovium TPPP3 51673 AQP1+ interstitial macrophages steady-state synovium APOE 348 CX3CR1+ lining macrophages steady-state synovium CAMK1 8536 CX3CR1+ lining macrophages steady-state synovium CCL3L3 414062 CX3CR1+ lining macrophages steady-state synovium CD83 9308 CX3CR1+ lining macrophages steady-state synovium CTSD 1509 CX3CR1+ lining macrophages steady-state synovium FN1 2335 CX3CR1+ lining macrophages steady-state synovium FOLR2 2350 CX3CR1+ lining macrophages steady-state synovium GRN 2896 CX3CR1+ lining macrophages steady-state synovium HEXB 3074 CX3CR1+ lining macrophages steady-state synovium LTC4S 4056 CX3CR1+ lining macrophages steady-state synovium LYZ 4069 CX3CR1+ lining macrophages steady-state synovium MAN2B1 4125 CX3CR1+ lining macrophages steady-state synovium NFKBIA 4792 CX3CR1+ lining macrophages steady-state synovium NUPR1 26471 CX3CR1+ lining macrophages steady-state synovium PLTP 5360 CX3CR1+ lining macrophages steady-state synovium S100B 6285 CX3CR1+ lining macrophages steady-state synovium SPARC 6678 CX3CR1+ lining macrophages steady-state synovium SRGN 5552 CX3CR1+ lining macrophages steady-state synovium SYNGR1 9145 CX3CR1+ lining macrophages steady-state synovium TIMP2 7077 CX3CR1+ lining macrophages steady-state synovium TMEM37 140738 CX3CR1+ lining macrophages steady-state synovium TREM2 54209 CX3CR1+ lining macrophages steady-state synovium VSIG4 11326 CX3CR1+ lining macrophages steady-state synovium CD52 1043 MHCII+ interstitial macrophages steady-state synovium CD74 972 MHCII+ interstitial macrophages steady-state synovium CLEC10A 10462 MHCII+ interstitial macrophages steady-state synovium CLEC4A 50856 MHCII+ interstitial macrophages steady-state synovium CORO1A 11151 MHCII+ interstitial macrophages steady-state synovium GM2A 2760 MHCII+ interstitial macrophages steady-state synovium HLA-DMA 3108 MHCII+ interstitial macrophages steady-state synovium HLA-DQA1 3117 MHCII+ interstitial macrophages steady-state synovium HLA-DQB1 3119 MHCII+ interstitial macrophages steady-state synovium HLA-DRB5 3127 MHCII+ interstitial macrophages steady-state synovium LSP1 4046 MHCII+ interstitial macrophages steady-state synovium PIM1 5292 MHCII+ interstitial macrophages steady-state synovium CCL13 6357 RELM-α+ interstitial macrophages steady-state synovium CCL7 6354 RELM-α+ interstitial macrophages steady-state synovium CXCL3 2921 RELM-α+ interstitial macrophages steady-state synovium DUSP1 1843 RELM-α+ interstitial macrophages steady-state synovium ZFP36 7538 RELM-α+ interstitial macrophages steady-state synovium JUNB 3726 RELM-α+ interstitial macrophages steady-state synovium PF4 5196 RELM-α+ interstitial macrophages steady-state synovium FOS 2353 RELM-α+ interstitial macrophages steady-state synovium ATF3 467 RELM-α+ interstitial macrophages steady-state synovium MT1A 4489 RELM-α+ interstitial macrophages steady-state synovium IER3 8870 RELM-α+ interstitial macrophages steady-state synovium CCL4 6351 RELM-α+ interstitial macrophages steady-state synovium NFKBIA 4792 RELM-α+ interstitial macrophages steady-state synovium CCL24 6369 RELM-α+ interstitial macrophages steady-state synovium MARCKSL1 65108 RELM-α+ interstitial macrophages steady-state synovium CXCL13 10563 RELM-α+ interstitial macrophages steady-state synovium JUN 3725 RELM-α+ interstitial macrophages steady-state synovium CCL3L3 414062 RELM-α+ interstitial macrophages steady-state synovium MT2A 4502 RELM-α+ interstitial macrophages steady-state synovium KLF6 1316 RELM-α+ interstitial macrophages steady-state synovium PIM1 5292 RELM-α+ interstitial macrophages steady-state synovium IFITM3 10410 RELM-α+ interstitial macrophages steady-state synovium CD83 9308 RELM-α+ interstitial macrophages steady-state synovium BTG2 7832 RELM-α+ interstitial macrophages steady-state synovium KLF4 9314 RELM-α+ interstitial macrophages steady-state synovium HSPA1A 3303 RELM-α+ interstitial macrophages steady-state synovium UBC 7316 RELM-α+ interstitial macrophages steady-state synovium IER2 9592 RELM-α+ interstitial macrophages steady-state synovium MRC1 4360 RELM-α+ interstitial macrophages steady-state synovium MCL1 4170 RELM-α+ interstitial macrophages steady-state synovium MAF 4094 RELM-α+ interstitial macrophages steady-state synovium ANXA1 301 STMN1+ proliferating cells steady-state synovium ANXA2 302 STMN1+ proliferating cells steady-state synovium ARL6IP1 23204 STMN1+ proliferating cells steady-state synovium ATP5IF1 93974 STMN1+ proliferating cells steady-state synovium BIRC5 332 STMN1+ proliferating cells steady-state synovium CBX3 11335 STMN1+ proliferating cells steady-state synovium CD74 972 STMN1+ proliferating cells steady-state synovium GAPDH 2597 STMN1+ proliferating cells steady-state synovium H2AFZ 3015 STMN1+ proliferating cells steady-state synovium HMGB1 3146 STMN1+ proliferating cells steady-state synovium HMGB2 3148 STMN1+ proliferating cells steady-state synovium HNRNPA3 79366 STMN1+ proliferating cells steady-state synovium JPT1 51155 STMN1+ proliferating cells steady-state synovium LDHA 3939 STMN1+ proliferating cells steady-state synovium LGALS1 3956 STMN1+ proliferating cells steady-state synovium LGALS3 3958 STMN1+ proliferating cells steady-state synovium MIF 4282 STMN1+ proliferating cells steady-state synovium NCL 4691 STMN1+ proliferating cells steady-state synovium NME1 4830 STMN1+ proliferating cells steady-state synovium NPM1 4869 STMN1+ proliferating cells steady-state synovium PKM 5315 STMN1+ proliferating cells steady-state synovium PLP2 5355 STMN1+ proliferating cells steady-state synovium PTMA 5757 STMN1+ proliferating cells steady-state synovium RAN 5901 STMN1+ proliferating cells steady-state synovium RANBP1 5902 STMN1+ proliferating cells steady-state synovium RBM3 5935 STMN1+ proliferating cells steady-state synovium S100A10 6281 STMN1+ proliferating cells steady-state synovium S100A11 6282 STMN1+ proliferating cells steady-state synovium SLC25A5 292 STMN1+ proliferating cells steady-state synovium SNRPE 6635 STMN1+ proliferating cells steady-state synovium SNRPG 6637 STMN1+ proliferating cells steady-state synovium STMN1 3925 STMN1+ proliferating cells steady-state synovium TAGLN2 8407 STMN1+ proliferating cells steady-state synovium TMSB10 9168 STMN1+ proliferating cells steady-state synovium TUBA1B 10376 STMN1+ proliferating cells steady-state synovium TUBA1C 84790 STMN1+ proliferating cells steady-state synovium TUBB 203068 STMN1+ proliferating cells steady-state synovium TUBB4B 10383 STMN1+ proliferating cells steady-state synovium TXN 7295 STMN1+ proliferating cells steady-state synovium UBE2C 11065 STMN1+ proliferating cells steady-state synovium VIM 7431 STMN1+ proliferating cells steady-state synovium ACTB 60 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ACTG1 71 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ACTR3 10096 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ADAM8 101 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ADORA2B 136 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ADSSL1 122622 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium AGPAT4 56895 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ALAS1 211 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ALDOA 226 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ALOX5AP 241 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ANKRD11 29123 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ANXA2 302 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium APRT 353 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ARF1 375 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ARF5 381 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ARHGDIB 397 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ARPC1B 10095 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ARPC2 10109 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ARPC3 10094 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ARPC4 10093 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ATF3 467 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ATP5C1 509 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ATP5F1 515 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium B4GALNT1 2583 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium BAK1 578 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium BIN2 51411 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium BIRC3 330 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium BTF3 689 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium BTG1 694 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium BTG2 7832 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium C19orf38 255809 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium C19orf53 28974 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium C5AR1 728 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium C5orf30 90355 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CAPZA2 830 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CAPZB 832 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CASP6 839 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CCDC12 151903 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CCL13 6357 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CCL3L3 414062 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CCND3 896 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CCNL1 57018 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CCR1 1230 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CCR2 729230 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CCRL2 9034 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CD14 929 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CD52 1043 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CD53 963 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CD86 942 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CDK2AP2 10263 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CDKN1A 1026 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CDKN2D 1032 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CFP 5199 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CHD7 55636 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CHMP4B 128866 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CISD2 493856 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CLEC4A 50856 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CLEC4D 338339 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CLEC4E 26253 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CLEC6A 93978 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CLIC1 1192 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CNN2 1265 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium COPE 11316 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CORO1A 11151 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CORO1B 57175 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium COTL1 23406 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CSF2RB 1439 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CTSC 1075 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CTSH 1512 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CXCL3 2921 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CYP4F2 8529 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium CYTIP 9595 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium DDX39A 10212 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium DENND4A 10260 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium DMKN 93099 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium DUSP1 1843 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium EIF3F 8665 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium EIF3H 8667 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium EIF3K 27335 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium EIF4A1 1973 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium EIF5A 1984 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium EMB 133418 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium EMD 2010 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium EMILIN2 84034 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ENO1 2023 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ERP44 23071 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ESD 2098 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium EVL 51466 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium F10 2159 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FAM107B 83641 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FAM49B 51571 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FAM96A 84191 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FAU 2197 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FCER1G 2207 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FCGR1A 2209 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FERMT3 83706 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FES 2242 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FGR 2268 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FIS1 51024 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FLOT1 10211 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FOS 2353 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FOSL2 2355 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FXYD5 53827 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium FYB 2533 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GADD45B 4616 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GADD45G 10912 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GAPDH 2597 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GCSH 2653 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GDA 9615 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GDI2 2665 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GLIPR2 152007 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GLRX 2745 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GM2A 2760 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GMFG 9535 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GNB2 2783 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GNGT2 2793 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GPR132 29933 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GSDMD 79792 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium GSR 2936 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium H2AFJ 55766 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium H2AFY 9555 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium H3F3A 3020 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HCK 3055 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HCLS1 3059 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HEBP1 50865 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HIF1A 3091 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HLA-DMA 3108 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HLA-DMB 3109 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HM13 81502 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HMGCL 3155 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HNRNPA3 220988 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HNRNPDL 9987 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HNRNPK 3190 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HP 3240 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HPCAL1 3241 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HSPA5 3309 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium HSPA8 3312 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ID2 3398 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IER3 8870 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IFI16 3428 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IFITM2 10581 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IFITM3 10410 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IFNAR2 3455 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IFNGR1 3459 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IFNGR2 3460 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IFRD1 3475 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IGSF6 10261 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IL17RA 23765 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IL18 3606 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IL1B 3553 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IL1RN 3557 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium IRF5 3663 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ISCU 23479 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ITGB2 3689 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ITGB7 3695 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium JARID2 3720 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium JUN 3725 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium JUNB 3726 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium KDM6B 23135 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium KDM7A 80853 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LDHA 3939 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LGALS3 3958 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LILRB3 11025 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LIMD2 80774 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LITAF 9516 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LMAN2 10960 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LMNB1 4001 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LRP10 26020 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LRRC25 126364 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LRRFIP1 9208 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LSP1 4046 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LTB4R 1241 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LY6E 4061 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium LYN 4067 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MANF 7873 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MAP2K3 5606 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MCUB 55013 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MEFV 4210 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MGST1 4257 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MILR1 284021 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MMP19 4327 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MPEG1 219972 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MRPL33 9553 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MRPL52 122704 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MSR1 4481 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MSRB1 51734 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MXD1 4084 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MYD88 4615 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MYL12A 10627 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium MYL12B 103910 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NAPSA 9476 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NCF2 4688 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NCF4 4689 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NDEL1 81565 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NDUFA3 4696 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NFE2L2 4780 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NFKBIA 4792 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NFKBIB 4793 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NFKBIZ 64332 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NMI 9111 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NOP53 29997 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NR4A1 3164 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NR4A2 4929 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium NRROS 375387 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium OSM 5008 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PDE4B 5142 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PDIA6 10130 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PGK1 5230 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PHLDA1 22822 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PICALM 8301 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PID1 55022 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PIM1 5292 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PITPNA 5306 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PKM 5315 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PLA2G7 7941 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PLAC8 51316 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PLAUR 5329 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PLBD1 79887 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PLD4 122618 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PLEK 5341 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PLIN2 123 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium POLD4 57804 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium POR 5447 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PPP1CA 5499 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PPP1R15A 23645 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PPP4C 5531 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PPT1 5538 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PRDX5 25824 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PRDX6 9588 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PSMA1 5682 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PSMA7 5688 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PSMB10 5699 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PSMB8 5696 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PSMB9 5698 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PSME1 5720 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PSME2 5721 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PSTPIP1 9051 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PTPN1 5770 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PTPN6 5777 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PTPRC 5788 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PXK 54899 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium PYCARD 29108 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RAB32 10981 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RAC2 5880 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RBM3 5935 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RBM39 9584 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RGCC 28984 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RGS2 5997 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RHOG 391 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RNF149 284996 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RNH1 6050 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RNPEP 6051 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL10 6134 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL13 6137 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL15 6138 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL17 6139 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL18 6141 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL18A 6142 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL19 6143 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL24 6152 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL27 6155 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL27A 6157 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL34 6164 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL36AL 6166 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL4 6124 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL8 6132 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPL9 6133 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPLP0 6175 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPS14 6208 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPS15A 6210 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPS16 6217 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPS18 6222 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPS19 6223 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPS27 6232 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPS27A 6233 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPS3 6188 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPS6 6194 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPS7 6201 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPS9 6203 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RPSA 3921 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium RUNX3 864 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium S100A11 6282 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SAMHD1 25939 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SBNO2 22904 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SCAND1 51282 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SDE2 163859 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SEC61B 10952 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SEC61G 23480 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SELPLG 6404 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SERP1 27230 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SF3B1 23451 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SF3B6 51639 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SHISA5 51246 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SIRPB1 10326 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SKAP2 8935 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SLC15A3 51296 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SLC16A3 9123 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SLC25A5 292 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SLC7A11 23657 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SLFN5 162394 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SMIM3 85027 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SMOX 54498 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SMPDL3A 10924 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SNX1 6642 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SOCS3 9021 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SOD2 6648 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SPCS2 9789 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SRGN 5552 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SRSF3 6428 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SRSF5 6430 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SSR2 6746 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ST3GAL4 6484 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SUB1 10923 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium SYS1 90196 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TALDO1 6888 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TARM1 441864 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TGFB1 7040 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TGFBI 7045 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TGIF1 7050 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TGM2 7052 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium THBS1 7057 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TKT 7086 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TLR2 7097 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TM6SF1 53346 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TMA7 51372 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TMBIM6 7009 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TMED2 10959 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TMED5 50999 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TMEM14C 51522 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TMEM167A 153339 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TMEM258 746 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TMSB10 9168 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TNFRSF1A 7132 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TOR1A 1861 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TOR1AIP1 26092 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TPD52 7163 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TPM4 7171 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TPST2 8459 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TRAF1 7185 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TRAM1 23471 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TREM1 54210 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TRIB1 10221 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TRPS1 7227 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TSPO 706 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TWF2 11344 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium TYROBP 7305 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium UBA52 7311 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium UBC 7316 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium UBE2D3 7323 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium UBE2L3 7332 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium UBE2N 7334 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium UCK2 7371 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium UCP2 7351 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium UQCRC1 7384 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium VAMP4 8674 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium VASP 7408 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium VCAN 1462 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium VMP1 81671 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium XBP1 7494 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ZBP1 81030 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ZEB2 9839 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ZFP36 7538 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ZNF705A 440077 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ZYX 7791 CCR2+IL1B+ infiltrating macrophages inflammatory arthritis synovium ABCA1 19 CX3CR1+ lining macrophages inflammatory arthritis synovium ABHD12 26090 CX3CR1+ lining macrophages inflammatory arthritis synovium ADAM15 8751 CX3CR1+ lining macrophages inflammatory arthritis synovium ADGRE5 976 CX3CR1+ lining macrophages inflammatory arthritis synovium AHNAK2 113146 CX3CR1+ lining macrophages inflammatory arthritis synovium AKR1B1 231 CX3CR1+ lining macrophages inflammatory arthritis synovium ALDH2 217 CX3CR1+ lining macrophages inflammatory arthritis synovium ALOX5 240 CX3CR1+ lining macrophages inflammatory arthritis synovium ANG 283 CX3CR1+ lining macrophages inflammatory arthritis synovium ANXA3 306 CX3CR1+ lining macrophages inflammatory arthritis synovium APOE 348 CX3CR1+ lining macrophages inflammatory arthritis synovium APP 351 CX3CR1+ lining macrophages inflammatory arthritis synovium ARL11 115761 CX3CR1+ lining macrophages inflammatory arthritis synovium ARSB 411 CX3CR1+ lining macrophages inflammatory arthritis synovium ASAH1 427 CX3CR1+ lining macrophages inflammatory arthritis synovium ASS1 445 CX3CR1+ lining macrophages inflammatory arthritis synovium ATP6AP1 537 CX3CR1+ lining macrophages inflammatory arthritis synovium ATRAID 51374 CX3CR1+ lining macrophages inflammatory arthritis synovium AXL 558 CX3CR1+ lining macrophages inflammatory arthritis synovium B2M 567 CX3CR1+ lining macrophages inflammatory arthritis synovium BCL2A1 597 CX3CR1+ lining macrophages inflammatory arthritis synovium BIN1 274 CX3CR1+ lining macrophages inflammatory arthritis synovium BLNK 29760 CX3CR1+ lining macrophages inflammatory arthritis synovium BLVRB 645 CX3CR1+ lining macrophages inflammatory arthritis synovium BMP2K 55589 CX3CR1+ lining macrophages inflammatory arthritis synovium C1QA 712 CX3CR1+ lining macrophages inflammatory arthritis synovium C1QB 713 CX3CR1+ lining macrophages inflammatory arthritis synovium C1QC 714 CX3CR1+ lining macrophages inflammatory arthritis synovium C3AR1 719 CX3CR1+ lining macrophages inflammatory arthritis synovium C3orf70 285382 CX3CR1+ lining macrophages inflammatory arthritis synovium C4B 721 CX3CR1+ lining macrophages inflammatory arthritis synovium C9orf3 84909 CX3CR1+ lining macrophages inflammatory arthritis synovium CAMK1 8536 CX3CR1+ lining macrophages inflammatory arthritis synovium CC2D1B 200014 CX3CR1+ lining macrophages inflammatory arthritis synovium CCL3L3 414062 CX3CR1+ lining macrophages inflammatory arthritis synovium CD109 135228 CX3CR1+ lining macrophages inflammatory arthritis synovium CD151 977 CX3CR1+ lining macrophages inflammatory arthritis synovium CD37 951 CX3CR1+ lining macrophages inflammatory arthritis synovium CD40 958 CX3CR1+ lining macrophages inflammatory arthritis synovium CD63 967 CX3CR1+ lining macrophages inflammatory arthritis synovium CD83 9308 CX3CR1+ lining macrophages inflammatory arthritis synovium CD84 8832 CX3CR1+ lining macrophages inflammatory arthritis synovium CD9 928 CX3CR1+ lining macrophages inflammatory arthritis synovium CDKN2C 1031 CX3CR1+ lining macrophages inflammatory arthritis synovium CEBPA 1050 CX3CR1+ lining macrophages inflammatory arthritis synovium CEBPG 1054 CX3CR1+ lining macrophages inflammatory arthritis synovium CEBPZOS 1.01E+08 CX3CR1+ lining macrophages inflammatory arthritis synovium CFH 3075 CX3CR1+ lining macrophages inflammatory arthritis synovium CHD9 80205 CX3CR1+ lining macrophages inflammatory arthritis synovium CHST1 8534 CX3CR1+ lining macrophages inflammatory arthritis synovium CLEC12A 160364 CX3CR1+ lining macrophages inflammatory arthritis synovium CLIC4 25932 CX3CR1+ lining macrophages inflammatory arthritis synovium COLEC12 81035 CX3CR1+ lining macrophages inflammatory arthritis synovium COMMD10 51397 CX3CR1+ lining macrophages inflammatory arthritis synovium COMT 1312 CX3CR1+ lining macrophages inflammatory arthritis synovium COTL1 23406 CX3CR1+ lining macrophages inflammatory arthritis synovium CREG1 8804 CX3CR1+ lining macrophages inflammatory arthritis synovium CRLF2 64109 CX3CR1+ lining macrophages inflammatory arthritis synovium CSF1R 1436 CX3CR1+ lining macrophages inflammatory arthritis synovium CSPG4 1464 CX3CR1+ lining macrophages inflammatory arthritis synovium CST3 1471 CX3CR1+ lining macrophages inflammatory arthritis synovium CTSA 5476 CX3CR1+ lining macrophages inflammatory arthritis synovium CTSB 1508 CX3CR1+ lining macrophages inflammatory arthritis synovium CTSD 1509 CX3CR1+ lining macrophages inflammatory arthritis synovium CTSF 8722 CX3CR1+ lining macrophages inflammatory arthritis synovium CTSS 1520 CX3CR1+ lining macrophages inflammatory arthritis synovium CX3CR1 1524 CX3CR1+ lining macrophages inflammatory arthritis synovium CYB5A 1528 CX3CR1+ lining macrophages inflammatory arthritis synovium CYFIP1 23191 CX3CR1+ lining macrophages inflammatory arthritis synovium DDX3X 1654 CX3CR1+ lining macrophages inflammatory arthritis synovium DHRS3 9249 CX3CR1+ lining macrophages inflammatory arthritis synovium DHRS7 51635 CX3CR1+ lining macrophages inflammatory arthritis synovium DNASE2 1777 CX3CR1+ lining macrophages inflammatory arthritis synovium DOK3 79930 CX3CR1+ lining macrophages inflammatory arthritis synovium DPP7 29952 CX3CR1+ lining macrophages inflammatory arthritis synovium DSTN 11034 CX3CR1+ lining macrophages inflammatory arthritis synovium DTNBP1 84062 CX3CR1+ lining macrophages inflammatory arthritis synovium DUSP3 1845 CX3CR1+ lining macrophages inflammatory arthritis synovium ECM1 1893 CX3CR1+ lining macrophages inflammatory arthritis synovium ECSCR 641700 CX3CR1+ lining macrophages inflammatory arthritis synovium EGR1 1958 CX3CR1+ lining macrophages inflammatory arthritis synovium ELMO1 9844 CX3CR1+ lining macrophages inflammatory arthritis synovium EMP3 2014 CX3CR1+ lining macrophages inflammatory arthritis synovium ENPP1 5167 CX3CR1+ lining macrophages inflammatory arthritis synovium ENTPD1 953 CX3CR1+ lining macrophages inflammatory arthritis synovium ERGIC3 51614 CX3CR1+ lining macrophages inflammatory arthritis synovium F11R 50848 CX3CR1+ lining macrophages inflammatory arthritis synovium FABP3 2170 CX3CR1+ lining macrophages inflammatory arthritis synovium FAM213B 127281 CX3CR1+ lining macrophages inflammatory arthritis synovium FAM3C 10447 CX3CR1+ lining macrophages inflammatory arthritis synovium FBXW4 6468 CX3CR1+ lining macrophages inflammatory arthritis synovium FCGRT 2217 CX3CR1+ lining macrophages inflammatory arthritis synovium FCHSD2 9873 CX3CR1+ lining macrophages inflammatory arthritis synovium FERMT2 10979 CX3CR1+ lining macrophages inflammatory arthritis synovium FEZ2 9637 CX3CR1+ lining macrophages inflammatory arthritis synovium FN1 2335 CX3CR1+ lining macrophages inflammatory arthritis synovium FOLR2 2350 CX3CR1+ lining macrophages inflammatory arthritis synovium FOSB 2354 CX3CR1+ lining macrophages inflammatory arthritis synovium FTH1 2495 CX3CR1+ lining macrophages inflammatory arthritis synovium FTL 2512 CX3CR1+ lining macrophages inflammatory arthritis synovium FUCA1 2517 CX3CR1+ lining macrophages inflammatory arthritis synovium GAS6 2621 CX3CR1+ lining macrophages inflammatory arthritis synovium GLMP 112770 CX3CR1+ lining macrophages inflammatory arthritis synovium GLTP 51228 CX3CR1+ lining macrophages inflammatory arthritis synovium GLUL 2752 CX3CR1+ lining macrophages inflammatory arthritis synovium GNA15 2769 CX3CR1+ lining macrophages inflammatory arthritis synovium GNAS 2778 CX3CR1+ lining macrophages inflammatory arthritis synovium GNG5 2787 CX3CR1+ lining macrophages inflammatory arthritis synovium GNS 2799 CX3CR1+ lining macrophages inflammatory arthritis synovium GPR34 2857 CX3CR1+ lining macrophages inflammatory arthritis synovium GPX1 2876 CX3CR1+ lining macrophages inflammatory arthritis synovium GPX4 2879 CX3CR1+ lining macrophages inflammatory arthritis synovium GRN 2896 CX3CR1+ lining macrophages inflammatory arthritis synovium GUSB 2990 CX3CR1+ lining macrophages inflammatory arthritis synovium HEXA 3073 CX3CR1+ lining macrophages inflammatory arthritis synovium HEXB 3074 CX3CR1+ lining macrophages inflammatory arthritis synovium HLA-A 3105 CX3CR1+ lining macrophages inflammatory arthritis synovium HPGD 3248 CX3CR1+ lining macrophages inflammatory arthritis synovium HPGDS 27306 CX3CR1+ lining macrophages inflammatory arthritis synovium HSBP1 3281 CX3CR1+ lining macrophages inflammatory arthritis synovium IER2 9592 CX3CR1+ lining macrophages inflammatory arthritis synovium IGF1 3479 CX3CR1+ lining macrophages inflammatory arthritis synovium IL11RA 3590 CX3CR1+ lining macrophages inflammatory arthritis synovium ITGAV 3685 CX3CR1+ lining macrophages inflammatory arthritis synovium ITGB1 3688 CX3CR1+ lining macrophages inflammatory arthritis synovium ITGB2 3689 CX3CR1+ lining macrophages inflammatory arthritis synovium ITGB5 3693 CX3CR1+ lining macrophages inflammatory arthritis synovium ITM2B 9445 CX3CR1+ lining macrophages inflammatory arthritis synovium ITM2C 81618 CX3CR1+ lining macrophages inflammatory arthritis synovium KCNK13 56659 CX3CR1+ lining macrophages inflammatory arthritis synovium KLC1 3831 CX3CR1+ lining macrophages inflammatory arthritis synovium KLF2 10365 CX3CR1+ lining macrophages inflammatory arthritis synovium KLF4 9314 CX3CR1+ lining macrophages inflammatory arthritis synovium KLHL6 89857 CX3CR1+ lining macrophages inflammatory arthritis synovium LAMP1 3916 CX3CR1+ lining macrophages inflammatory arthritis synovium LAMP2 3920 CX3CR1+ lining macrophages inflammatory arthritis synovium LAMTOR1 55004 CX3CR1+ lining macrophages inflammatory arthritis synovium LAPTM4A 9741 CX3CR1+ lining macrophages inflammatory arthritis synovium LGALS9B 284194 CX3CR1+ lining macrophages inflammatory arthritis synovium LGMN 5641 CX3CR1+ lining macrophages inflammatory arthritis synovium LIPA 3988 CX3CR1+ lining macrophages inflammatory arthritis synovium LMO2 4005 CX3CR1+ lining macrophages inflammatory arthritis synovium LPCAT2 54947 CX3CR1+ lining macrophages inflammatory arthritis synovium LRP1 4035 CX3CR1+ lining macrophages inflammatory arthritis synovium LTC4S 4056 CX3CR1+ lining macrophages inflammatory arthritis synovium LUZP1 7798 CX3CR1+ lining macrophages inflammatory arthritis synovium LY86 9450 CX3CR1+ lining macrophages inflammatory arthritis synovium LYL1 4066 CX3CR1+ lining macrophages inflammatory arthritis synovium LYVE1 10894 CX3CR1+ lining macrophages inflammatory arthritis synovium LYZ 4069 CX3CR1+ lining macrophages inflammatory arthritis synovium MACF1 23499 CX3CR1+ lining macrophages inflammatory arthritis synovium MAF 4094 CX3CR1+ lining macrophages inflammatory arthritis synovium MAN2B1 4125 CX3CR1+ lining macrophages inflammatory arthritis synovium MAP1LC3A 84557 CX3CR1+ lining macrophages inflammatory arthritis synovium MAPK3 5595 CX3CR1+ lining macrophages inflammatory arthritis synovium MARCKS 4082 CX3CR1+ lining macrophages inflammatory arthritis synovium MDH1 4190 CX3CR1+ lining macrophages inflammatory arthritis synovium MEF2A 4205 CX3CR1+ lining macrophages inflammatory arthritis synovium MEF2C 4208 CX3CR1+ lining macrophages inflammatory arthritis synovium MFGE8 4240 CX3CR1+ lining macrophages inflammatory arthritis synovium MGST1 4257 CX3CR1+ lining macrophages inflammatory arthritis synovium MGST3 4259 CX3CR1+ lining macrophages inflammatory arthritis synovium MOB2 81532 CX3CR1+ lining macrophages inflammatory arthritis synovium MPP1 4354 CX3CR1+ lining macrophages inflammatory arthritis synovium MS4A7 58475 CX3CR1+ lining macrophages inflammatory arthritis synovium MT-ND2 4536 CX3CR1+ lining macrophages inflammatory arthritis synovium MTDH 92140 CX3CR1+ lining macrophages inflammatory arthritis synovium MTUS1 57509 CX3CR1+ lining macrophages inflammatory arthritis synovium NAGK 55577 CX3CR1+ lining macrophages inflammatory arthritis synovium NCF1 653361 CX3CR1+ lining macrophages inflammatory arthritis synovium NECAP2 55707 CX3CR1+ lining macrophages inflammatory arthritis synovium NFIA 4774 CX3CR1+ lining macrophages inflammatory arthritis synovium NFIC 4782 CX3CR1+ lining macrophages inflammatory arthritis synovium NINJ1 4814 CX3CR1+ lining macrophages inflammatory arthritis synovium NPC2 10577 CX3CR1+ lining macrophages inflammatory arthritis synovium NPL 80896 CX3CR1+ lining macrophages inflammatory arthritis synovium NPTN 27020 CX3CR1+ lining macrophages inflammatory arthritis synovium NRP1 8829 CX3CR1+ lining macrophages inflammatory arthritis synovium NTPCR 84284 CX3CR1+ lining macrophages inflammatory arthritis synovium NUCB1 4924 CX3CR1+ lining macrophages inflammatory arthritis synovium NUPR1 26471 CX3CR1+ lining macrophages inflammatory arthritis synovium OLFML3 56944 CX3CR1+ lining macrophages inflammatory arthritis synovium OPHN1 4983 CX3CR1+ lining macrophages inflammatory arthritis synovium P2RX4 5025 CX3CR1+ lining macrophages inflammatory arthritis synovium P2RY12 64805 CX3CR1+ lining macrophages inflammatory arthritis synovium P2RY6 5031 CX3CR1+ lining macrophages inflammatory arthritis synovium PALD1 27143 CX3CR1+ lining macrophages inflammatory arthritis synovium PBXIP1 57326 CX3CR1+ lining macrophages inflammatory arthritis synovium PDLIM2 64236 CX3CR1+ lining macrophages inflammatory arthritis synovium PDLIM7 9260 CX3CR1+ lining macrophages inflammatory arthritis synovium PEPD 5184 CX3CR1+ lining macrophages inflammatory arthritis synovium PKIB 5570 CX3CR1+ lining macrophages inflammatory arthritis synovium PLA2G15 23659 CX3CR1+ lining macrophages inflammatory arthritis synovium PLA2G16 11145 CX3CR1+ lining macrophages inflammatory arthritis synovium PLBD2 196463 CX3CR1+ lining macrophages inflammatory arthritis synovium PLOD1 5351 CX3CR1+ lining macrophages inflammatory arthritis synovium PLTP 5360 CX3CR1+ lining macrophages inflammatory arthritis synovium PLXNB2 23654 CX3CR1+ lining macrophages inflammatory arthritis synovium PMEPA1 56937 CX3CR1+ lining macrophages inflammatory arthritis synovium PMP22 5376 CX3CR1+ lining macrophages inflammatory arthritis synovium PNKD 25953 CX3CR1+ lining macrophages inflammatory arthritis synovium POLR2E 5434 CX3CR1+ lining macrophages inflammatory arthritis synovium PON2 5445 CX3CR1+ lining macrophages inflammatory arthritis synovium PON3 5446 CX3CR1+ lining macrophages inflammatory arthritis synovium PRUNE2 158471 CX3CR1+ lining macrophages inflammatory arthritis synovium PTPRA 5786 CX3CR1+ lining macrophages inflammatory arthritis synovium QKI 9444 CX3CR1+ lining macrophages inflammatory arthritis synovium QPCT 25797 CX3CR1+ lining macrophages inflammatory arthritis synovium RAB11A 8766 CX3CR1+ lining macrophages inflammatory arthritis synovium RAB11FIP5 26056 CX3CR1+ lining macrophages inflammatory arthritis synovium RAB31 11031 CX3CR1+ lining macrophages inflammatory arthritis synovium RAB3IL1 5866 CX3CR1+ lining macrophages inflammatory arthritis synovium RABAC1 10567 CX3CR1+ lining macrophages inflammatory arthritis synovium RASGEF1B 153020 CX3CR1+ lining macrophages inflammatory arthritis synovium RASGRP3 25780 CX3CR1+ lining macrophages inflammatory arthritis synovium RENBP 5973 CX3CR1+ lining macrophages inflammatory arthritis synovium RFTN1 23180 CX3CR1+ lining macrophages inflammatory arthritis synovium RGS10 6001 CX3CR1+ lining macrophages inflammatory arthritis synovium RHOA 387 CX3CR1+ lining macrophages inflammatory arthritis synovium RHOB 388 CX3CR1+ lining macrophages inflammatory arthritis synovium RHOC 389 CX3CR1+ lining macrophages inflammatory arthritis synovium RIN2 54453 CX3CR1+ lining macrophages inflammatory arthritis synovium RNASE4 6038 CX3CR1+ lining macrophages inflammatory arthritis synovium RNASET2 8635 CX3CR1+ lining macrophages inflammatory arthritis synovium RNF13 11342 CX3CR1+ lining macrophages inflammatory arthritis synovium RTCB 51493 CX3CR1+ lining macrophages inflammatory arthritis synovium S100A1 6271 CX3CR1+ lining macrophages inflammatory arthritis synovium S100A13 6284 CX3CR1+ lining macrophages inflammatory arthritis synovium S100B 6285 CX3CR1+ lining macrophages inflammatory arthritis synovium S1PR1 1901 CX3CR1+ lining macrophages inflammatory arthritis synovium SAMD9L 219285 CX3CR1+ lining macrophages inflammatory arthritis synovium SARAF 51669 CX3CR1+ lining macrophages inflammatory arthritis synovium SASH1 23328 CX3CR1+ lining macrophages inflammatory arthritis synovium SAT1 6303 CX3CR1+ lining macrophages inflammatory arthritis synovium SCAMP2 10066 CX3CR1+ lining macrophages inflammatory arthritis synovium SCOC 60592 CX3CR1+ lining macrophages inflammatory arthritis synovium SEC14L1 6397 CX3CR1+ lining macrophages inflammatory arthritis synovium SELENBP1 8991 CX3CR1+ lining macrophages inflammatory arthritis synovium SELENOM 140606 CX3CR1+ lining macrophages inflammatory arthritis synovium SELENOP 6414 CX3CR1+ lining macrophages inflammatory arthritis synovium SELENOW 6415 CX3CR1+ lining macrophages inflammatory arthritis synovium SERINC3 10955 CX3CR1+ lining macrophages inflammatory arthritis synovium SERPINB6 5269 CX3CR1+ lining macrophages inflammatory arthritis synovium SERPINE1 5054 CX3CR1+ lining macrophages inflammatory arthritis synovium SESN1 27244 CX3CR1+ lining macrophages inflammatory arthritis synovium SFXN3 81855 CX3CR1+ lining macrophages inflammatory arthritis synovium SGK1 6446 CX3CR1+ lining macrophages inflammatory arthritis synovium SH3BP5 9467 CX3CR1+ lining macrophages inflammatory arthritis synovium SH3GLB1 51100 CX3CR1+ lining macrophages inflammatory arthritis synovium SIGMAR1 10280 CX3CR1+ lining macrophages inflammatory arthritis synovium SIRT2 22933 CX3CR1+ lining macrophages inflammatory arthritis synovium SKI 6497 CX3CR1+ lining macrophages inflammatory arthritis synovium SKIL 6498 CX3CR1+ lining macrophages inflammatory arthritis synovium SLC27A1 376497 CX3CR1+ lining macrophages inflammatory arthritis synovium SLC29A1 2030 CX3CR1+ lining macrophages inflammatory arthritis synovium SLC2A6 11182 CX3CR1+ lining macrophages inflammatory arthritis synovium SLC6A6 6533 CX3CR1+ lining macrophages inflammatory arthritis synovium SLC9A3R2 9351 CX3CR1+ lining macrophages inflammatory arthritis synovium SLCO2B1 11309 CX3CR1+ lining macrophages inflammatory arthritis synovium SMAGP 57228 CX3CR1+ lining macrophages inflammatory arthritis synovium SMIM14 201895 CX3CR1+ lining macrophages inflammatory arthritis synovium SNX3 8724 CX3CR1+ lining macrophages inflammatory arthritis synovium SPARC 6678 CX3CR1+ lining macrophages inflammatory arthritis synovium SPTBN1 6711 CX3CR1+ lining macrophages inflammatory arthritis synovium SPTSSA 171546 CX3CR1+ lining macrophages inflammatory arthritis synovium SRGAP2 23380 CX3CR1+ lining macrophages inflammatory arthritis synovium SSBP4 170463 CX3CR1+ lining macrophages inflammatory arthritis synovium ST3GAL5 8869 CX3CR1+ lining macrophages inflammatory arthritis synovium STAB1 23166 CX3CR1+ lining macrophages inflammatory arthritis synovium STOM 2040 CX3CR1+ lining macrophages inflammatory arthritis synovium STX4 6810 CX3CR1+ lining macrophages inflammatory arthritis synovium SULF2 55959 CX3CR1+ lining macrophages inflammatory arthritis synovium SYNGR1 9145 CX3CR1+ lining macrophages inflammatory arthritis synovium TBXAS1 6916 CX3CR1+ lining macrophages inflammatory arthritis synovium TCIM 56892 CX3CR1+ lining macrophages inflammatory arthritis synovium TCN2 6948 CX3CR1+ lining macrophages inflammatory arthritis synovium TECR 9524 CX3CR1+ lining macrophages inflammatory arthritis synovium TGFBR1 7046 CX3CR1+ lining macrophages inflammatory arthritis synovium TGFBR2 7048 CX3CR1+ lining macrophages inflammatory arthritis synovium TIMD4 91937 CX3CR1+ lining macrophages inflammatory arthritis synovium TIMP2 7077 CX3CR1+ lining macrophages inflammatory arthritis synovium TMBIM1 64114 CX3CR1+ lining macrophages inflammatory arthritis synovium TMEM141 85014 CX3CR1+ lining macrophages inflammatory arthritis synovium TMEM176B 28959 CX3CR1+ lining macrophages inflammatory arthritis synovium TMEM37 140738 CX3CR1+ lining macrophages inflammatory arthritis synovium TMEM50A 23585 CX3CR1+ lining macrophages inflammatory arthritis synovium TMEM59 9528 CX3CR1+ lining macrophages inflammatory arthritis synovium TMEM86A 144110 CX3CR1+ lining macrophages inflammatory arthritis synovium TMEM9B 56674 CX3CR1+ lining macrophages inflammatory arthritis synovium TMSB4X 7114 CX3CR1+ lining macrophages inflammatory arthritis synovium TNFRSF21 27242 CX3CR1+ lining macrophages inflammatory arthritis synovium TNFSF12 8742 CX3CR1+ lining macrophages inflammatory arthritis synovium TNS1 7145 CX3CR1+ lining macrophages inflammatory arthritis synovium TPP1 1200 CX3CR1+ lining macrophages inflammatory arthritis synovium TREM2 54209 CX3CR1+ lining macrophages inflammatory arthritis synovium TSC22D3 1831 CX3CR1+ lining macrophages inflammatory arthritis synovium TSPAN3 10099 CX3CR1+ lining macrophages inflammatory arthritis synovium TSPAN4 7106 CX3CR1+ lining macrophages inflammatory arthritis synovium TUBA1A 7846 CX3CR1+ lining macrophages inflammatory arthritis synovium UBXN1 51035 CX3CR1+ lining macrophages inflammatory arthritis synovium UCHL3 7347 CX3CR1+ lining macrophages inflammatory arthritis synovium VAT1 10493 CX3CR1+ lining macrophages inflammatory arthritis synovium VSIG4 11326 CX3CR1+ lining macrophages inflammatory arthritis synovium YPEL3 83719 CX3CR1+ lining macrophages inflammatory arthritis synovium ZBTB20 26137 CX3CR1+ lining macrophages inflammatory arthritis synovium ZFHX3 463 CX3CR1+ lining macrophages inflammatory arthritis synovium ZMIZ1 57178 CX3CR1+ lining macrophages inflammatory arthritis synovium ABCA9 10350 RELM-α+ interstitial macrophages inflammatory arthritis synovium ABHD12 26090 RELM-α+ interstitial macrophages inflammatory arthritis synovium ACAT1 38 RELM-α+ interstitial macrophages inflammatory arthritis synovium ACOT13 55856 RELM-α+ interstitial macrophages inflammatory arthritis synovium AHNAK 79026 RELM-α+ interstitial macrophages inflammatory arthritis synovium AHNAK2 113146 RELM-α+ interstitial macrophages inflammatory arthritis synovium AKR1B1 231 RELM-α+ interstitial macrophages inflammatory arthritis synovium ALDH2 217 RELM-α+ interstitial macrophages inflammatory arthritis synovium ALOX5 240 RELM-α+ interstitial macrophages inflammatory arthritis synovium ANG 283 RELM-α+ interstitial macrophages inflammatory arthritis synovium ANP32A 8125 RELM-α+ interstitial macrophages inflammatory arthritis synovium ANXA11 311 RELM-α+ interstitial macrophages inflammatory arthritis synovium ANXA6 309 RELM-α+ interstitial macrophages inflammatory arthritis synovium AP1B1 162 RELM-α+ interstitial macrophages inflammatory arthritis synovium AP2A2 161 RELM-α+ interstitial macrophages inflammatory arthritis synovium AP2M1 1173 RELM-α+ interstitial macrophages inflammatory arthritis synovium APLP2 334 RELM-α+ interstitial macrophages inflammatory arthritis synovium AQP1 358 RELM-α+ interstitial macrophages inflammatory arthritis synovium ATRAID 51374 RELM-α+ interstitial macrophages inflammatory arthritis synovium BIN1 274 RELM-α+ interstitial macrophages inflammatory arthritis synovium BLVRB 645 RELM-α+ interstitial macrophages inflammatory arthritis synovium BORCS6 54785 RELM-α+ interstitial macrophages inflammatory arthritis synovium C16orf54 283897 RELM-α+ interstitial macrophages inflammatory arthritis synovium C1QA 712 RELM-α+ interstitial macrophages inflammatory arthritis synovium C1QB 713 RELM-α+ interstitial macrophages inflammatory arthritis synovium C1QC 714 RELM-α+ interstitial macrophages inflammatory arthritis synovium C4B 721 RELM-α+ interstitial macrophages inflammatory arthritis synovium CALM2 805 RELM-α+ interstitial macrophages inflammatory arthritis synovium CAVIN1 284119 RELM-α+ interstitial macrophages inflammatory arthritis synovium CCL24 6369 RELM-α+ interstitial macrophages inflammatory arthritis synovium CD163 9332 RELM-α+ interstitial macrophages inflammatory arthritis synovium CD302 9936 RELM-α+ interstitial macrophages inflammatory arthritis synovium CD36 948 RELM-α+ interstitial macrophages inflammatory arthritis synovium CD37 951 RELM-α+ interstitial macrophages inflammatory arthritis synovium CD48 962 RELM-α+ interstitial macrophages inflammatory arthritis synovium CD63 967 RELM-α+ interstitial macrophages inflammatory arthritis synovium CD74 972 RELM-α+ interstitial macrophages inflammatory arthritis synovium CD81 975 RELM-α+ interstitial macrophages inflammatory arthritis synovium CDKN2C 1031 RELM-α+ interstitial macrophages inflammatory arthritis synovium CFH 3075 RELM-α+ interstitial macrophages inflammatory arthritis synovium CLEC10A 10462 RELM-α+ interstitial macrophages inflammatory arthritis synovium CLN8 2055 RELM-α+ interstitial macrophages inflammatory arthritis synovium CLTA 1211 RELM-α+ interstitial macrophages inflammatory arthritis synovium CLTB 1212 RELM-α+ interstitial macrophages inflammatory arthritis synovium CLTC 1213 RELM-α+ interstitial macrophages inflammatory arthritis synovium CNPY2 10330 RELM-α+ interstitial macrophages inflammatory arthritis synovium COLEC12 81035 RELM-α+ interstitial macrophages inflammatory arthritis synovium COMT 1312 RELM-α+ interstitial macrophages inflammatory arthritis synovium CRACR2B 283229 RELM-α+ interstitial macrophages inflammatory arthritis synovium CSF1R 1436 RELM-α+ interstitial macrophages inflammatory arthritis synovium CST3 1471 RELM-α+ interstitial macrophages inflammatory arthritis synovium CTSB 1508 RELM-α+ interstitial macrophages inflammatory arthritis synovium CTSC 1075 RELM-α+ interstitial macrophages inflammatory arthritis synovium CYB5A 1528 RELM-α+ interstitial macrophages inflammatory arthritis synovium CYB5R3 1727 RELM-α+ interstitial macrophages inflammatory arthritis synovium DAB2 1601 RELM-α+ interstitial macrophages inflammatory arthritis synovium DGUOK 1716 RELM-α+ interstitial macrophages inflammatory arthritis synovium DHRS3 9249 RELM-α+ interstitial macrophages inflammatory arthritis synovium DNASE1L1 1774 RELM-α+ interstitial macrophages inflammatory arthritis synovium DOK2 9046 RELM-α+ interstitial macrophages inflammatory arthritis synovium DSE 29940 RELM-α+ interstitial macrophages inflammatory arthritis synovium DSTN 11034 RELM-α+ interstitial macrophages inflammatory arthritis synovium DUSP22 56940 RELM-α+ interstitial macrophages inflammatory arthritis synovium DUSP6 1848 RELM-α+ interstitial macrophages inflammatory arthritis synovium ECM1 1893 RELM-α+ interstitial macrophages inflammatory arthritis synovium EHD4 30844 RELM-α+ interstitial macrophages inflammatory arthritis synovium EID1 23741 RELM-α+ interstitial macrophages inflammatory arthritis synovium EPS15 2060 RELM-α+ interstitial macrophages inflammatory arthritis synovium EPS8 2059 RELM-α+ interstitial macrophages inflammatory arthritis synovium ETV1 2115 RELM-α+ interstitial macrophages inflammatory arthritis synovium EVI5 7813 RELM-α+ interstitial macrophages inflammatory arthritis synovium F13A1 2162 RELM-α+ interstitial macrophages inflammatory arthritis synovium FAM46A 55603 RELM-α+ interstitial macrophages inflammatory arthritis synovium FCGR2A 2212 RELM-α+ interstitial macrophages inflammatory arthritis synovium FCGR2B 2213 RELM-α+ interstitial macrophages inflammatory arthritis synovium FCGRT 2217 RELM-α+ interstitial macrophages inflammatory arthritis synovium FCHO2 115548 RELM-α+ interstitial macrophages inflammatory arthritis synovium FEZ2 9637 RELM-α+ interstitial macrophages inflammatory arthritis synovium FGFR1 2260 RELM-α+ interstitial macrophages inflammatory arthritis synovium FKBP1A 2280 RELM-α+ interstitial macrophages inflammatory arthritis synovium FNTA 2339 RELM-α+ interstitial macrophages inflammatory arthritis synovium FOLR2 2350 RELM-α+ interstitial macrophages inflammatory arthritis synovium FOXN3 1112 RELM-α+ interstitial macrophages inflammatory arthritis synovium FOXP1 27086 RELM-α+ interstitial macrophages inflammatory arthritis synovium FRMD4B 23150 RELM-α+ interstitial macrophages inflammatory arthritis synovium FXYD2 486 RELM-α+ interstitial macrophages inflammatory arthritis synovium GABARAPL1 23710 RELM-α+ interstitial macrophages inflammatory arthritis synovium GAS6 2621 RELM-α+ interstitial macrophages inflammatory arthritis synovium GAS7 8522 RELM-α+ interstitial macrophages inflammatory arthritis synovium GATM 2628 RELM-α+ interstitial macrophages inflammatory arthritis synovium GLTP 51228 RELM-α+ interstitial macrophages inflammatory arthritis synovium GLUL 2752 RELM-α+ interstitial macrophages inflammatory arthritis synovium GPR34 2857 RELM-α+ interstitial macrophages inflammatory arthritis synovium GSTM5 2949 RELM-α+ interstitial macrophages inflammatory arthritis synovium GYPC 2995 RELM-α+ interstitial macrophages inflammatory arthritis synovium H2AFV 94239 RELM-α+ interstitial macrophages inflammatory arthritis synovium HACD4 401494 RELM-α+ interstitial macrophages inflammatory arthritis synovium HCST 10870 RELM-α+ interstitial macrophages inflammatory arthritis synovium HEXA 3073 RELM-α+ interstitial macrophages inflammatory arthritis synovium HFE 3077 RELM-α+ interstitial macrophages inflammatory arthritis synovium HIGD2A 192286 RELM-α+ interstitial macrophages inflammatory arthritis synovium HIST1H2BI 8346 RELM-α+ interstitial macrophages inflammatory arthritis synovium HMGN1 3150 RELM-α+ interstitial macrophages inflammatory arthritis synovium HMOX2 3163 RELM-α+ interstitial macrophages inflammatory arthritis synovium HP1BP3 50809 RELM-α+ interstitial macrophages inflammatory arthritis synovium HPGD 3248 RELM-α+ interstitial macrophages inflammatory arthritis synovium HPGDS 27306 RELM-α+ interstitial macrophages inflammatory arthritis synovium HPRT1 3251 RELM-α+ interstitial macrophages inflammatory arthritis synovium IDH2 3418 RELM-α+ interstitial macrophages inflammatory arthritis synovium IFI16 3428 RELM-α+ interstitial macrophages inflammatory arthritis synovium IGF1 3479 RELM-α+ interstitial macrophages inflammatory arthritis synovium IGFBP4 3487 RELM-α+ interstitial macrophages inflammatory arthritis synovium IGHM 3507 RELM-α+ interstitial macrophages inflammatory arthritis synovium ITM2B 9445 RELM-α+ interstitial macrophages inflammatory arthritis synovium ITPRIPL2 162073 RELM-α+ interstitial macrophages inflammatory arthritis synovium ITSN1 6453 RELM-α+ interstitial macrophages inflammatory arthritis synovium KIAA0100 9703 RELM-α+ interstitial macrophages inflammatory arthritis synovium KIF1B 23095 RELM-α+ interstitial macrophages inflammatory arthritis synovium LAMP1 3916 RELM-α+ interstitial macrophages inflammatory arthritis synovium LAMP2 3920 RELM-α+ interstitial macrophages inflammatory arthritis synovium LAPTM4A 9741 RELM-α+ interstitial macrophages inflammatory arthritis synovium LEPROT 54741 RELM-α+ interstitial macrophages inflammatory arthritis synovium LGMN 5641 RELM-α+ interstitial macrophages inflammatory arthritis synovium LIFR 3977 RELM-α+ interstitial macrophages inflammatory arthritis synovium LIPA 3988 RELM-α+ interstitial macrophages inflammatory arthritis synovium LTC4S 4056 RELM-α+ interstitial macrophages inflammatory arthritis synovium LY96 23643 RELM-α+ interstitial macrophages inflammatory arthritis synovium LYL1 4066 RELM-α+ interstitial macrophages inflammatory arthritis synovium LYVE1 10894 RELM-α+ interstitial macrophages inflammatory arthritis synovium MAF 4094 RELM-α+ interstitial macrophages inflammatory arthritis synovium MAFB 9935 RELM-α+ interstitial macrophages inflammatory arthritis synovium MALAT1 378938 RELM-α+ interstitial macrophages inflammatory arthritis synovium MAN1A1 4121 RELM-α+ interstitial macrophages inflammatory arthritis synovium MBNL1 4154 RELM-α+ interstitial macrophages inflammatory arthritis synovium MEF2C 4208 RELM-α+ interstitial macrophages inflammatory arthritis synovium MGST3 4259 RELM-α+ interstitial macrophages inflammatory arthritis synovium MID1IP1 58526 RELM-α+ interstitial macrophages inflammatory arthritis synovium MINDY2 54629 RELM-α+ interstitial macrophages inflammatory arthritis synovium MPP1 4354 RELM-α+ interstitial macrophages inflammatory arthritis synovium MRC1 4360 RELM-α+ interstitial macrophages inflammatory arthritis synovium MRFAP1 93621 RELM-α+ interstitial macrophages inflammatory arthritis synovium MTSS1 9788 RELM-α+ interstitial macrophages inflammatory arthritis synovium MYO5A 4644 RELM-α+ interstitial macrophages inflammatory arthritis synovium NCOA4 8031 RELM-α+ interstitial macrophages inflammatory arthritis synovium NDFIP1 80762 RELM-α+ interstitial macrophages inflammatory arthritis synovium NDUFS7 374291 RELM-α+ interstitial macrophages inflammatory arthritis synovium NENF 29937 RELM-α+ interstitial macrophages inflammatory arthritis synovium NINJ1 4814 RELM-α+ interstitial macrophages inflammatory arthritis synovium NISCH 11188 RELM-α+ interstitial macrophages inflammatory arthritis synovium NPL 80896 RELM-α+ interstitial macrophages inflammatory arthritis synovium NR3C1 2908 RELM-α+ interstitial macrophages inflammatory arthritis synovium NRP1 8829 RELM-α+ interstitial macrophages inflammatory arthritis synovium NUDT9 53343 RELM-α+ interstitial macrophages inflammatory arthritis synovium OAT 4942 RELM-α+ interstitial macrophages inflammatory arthritis synovium P2RY12 64805 RELM-α+ interstitial macrophages inflammatory arthritis synovium P2RY6 5031 RELM-α+ interstitial macrophages inflammatory arthritis synovium PDLIM1 9124 RELM-α+ interstitial macrophages inflammatory arthritis synovium PDLIM4 8572 RELM-α+ interstitial macrophages inflammatory arthritis synovium PEA15 8682 RELM-α+ interstitial macrophages inflammatory arthritis synovium PEPD 5184 RELM-α+ interstitial macrophages inflammatory arthritis synovium PF4 5196 RELM-α+ interstitial macrophages inflammatory arthritis synovium PGRMC1 10857 RELM-α+ interstitial macrophages inflammatory arthritis synovium PINK1 65018 RELM-α+ interstitial macrophages inflammatory arthritis synovium PKIG 11142 RELM-α+ interstitial macrophages inflammatory arthritis synovium PLTP 5360 RELM-α+ interstitial macrophages inflammatory arthritis synovium PMP22 5376 RELM-α+ interstitial macrophages inflammatory arthritis synovium POLR3GL 84265 RELM-α+ interstitial macrophages inflammatory arthritis synovium PON2 5445 RELM-α+ interstitial macrophages inflammatory arthritis synovium PPIA 5478 RELM-α+ interstitial macrophages inflammatory arthritis synovium PPP3CA 5530 RELM-α+ interstitial macrophages inflammatory arthritis synovium PRCP 5547 RELM-α+ interstitial macrophages inflammatory arthritis synovium PROS1 5627 RELM-α+ interstitial macrophages inflammatory arthritis synovium PRUNE2 158471 RELM-α+ interstitial macrophages inflammatory arthritis synovium PSD3 23362 RELM-α+ interstitial macrophages inflammatory arthritis synovium PTAFR 5724 RELM-α+ interstitial macrophages inflammatory arthritis synovium PTPN18 26469 RELM-α+ interstitial macrophages inflammatory arthritis synovium PTS 5805 RELM-α+ interstitial macrophages inflammatory arthritis synovium QPCT 25797 RELM-α+ interstitial macrophages inflammatory arthritis synovium RAB11A 8766 RELM-α+ interstitial macrophages inflammatory arthritis synovium RAB11FIP5 26056 RELM-α+ interstitial macrophages inflammatory arthritis synovium RAB31 11031 RELM-α+ interstitial macrophages inflammatory arthritis synovium RABAC1 10567 RELM-α+ interstitial macrophages inflammatory arthritis synovium RALBP1 10928 RELM-α+ interstitial macrophages inflammatory arthritis synovium RAPGEF6 51735 RELM-α+ interstitial macrophages inflammatory arthritis synovium RASGRP3 25780 RELM-α+ interstitial macrophages inflammatory arthritis synovium RASSF4 83937 RELM-α+ interstitial macrophages inflammatory arthritis synovium RFK 55312 RELM-α+ interstitial macrophages inflammatory arthritis synovium RGL1 23179 RELM-α+ interstitial macrophages inflammatory arthritis synovium RGS10 6001 RELM-α+ interstitial macrophages inflammatory arthritis synovium RGS18 64407 RELM-α+ interstitial macrophages inflammatory arthritis synovium RIN2 54453 RELM-α+ interstitial macrophages inflammatory arthritis synovium RNASE4 6038 RELM-α+ interstitial macrophages inflammatory arthritis synovium RNF13 11342 RELM-α+ interstitial macrophages inflammatory arthritis synovium RNF130 55819 RELM-α+ interstitial macrophages inflammatory arthritis synovium RSRP1 57035 RELM-α+ interstitial macrophages inflammatory arthritis synovium S100A1 6271 RELM-α+ interstitial macrophages inflammatory arthritis synovium S1PR1 1901 RELM-α+ interstitial macrophages inflammatory arthritis synovium SBDS 51119 RELM-α+ interstitial macrophages inflammatory arthritis synovium SCAMP2 10066 RELM-α+ interstitial macrophages inflammatory arthritis synovium SDHC 6391 RELM-α+ interstitial macrophages inflammatory arthritis synovium SEC14L1 6397 RELM-α+ interstitial macrophages inflammatory arthritis synovium SEC62 7095 RELM-α+ interstitial macrophages inflammatory arthritis synovium SELENBP1 8991 RELM-α+ interstitial macrophages inflammatory arthritis synovium SELENOF 9403 RELM-α+ interstitial macrophages inflammatory arthritis synovium SELENOM 140606 RELM-α+ interstitial macrophages inflammatory arthritis synovium SELENOP 6414 RELM-α+ interstitial macrophages inflammatory arthritis synovium SERINC3 10955 RELM-α+ interstitial macrophages inflammatory arthritis synovium SERPINB1 1992 RELM-α+ interstitial macrophages inflammatory arthritis synovium SERPINB6 5269 RELM-α+ interstitial macrophages inflammatory arthritis synovium SESN1 27244 RELM-α+ interstitial macrophages inflammatory arthritis synovium SGPP1 81537 RELM-α+ interstitial macrophages inflammatory arthritis synovium SH3BGRL 6451 RELM-α+ interstitial macrophages inflammatory arthritis synovium SLC29A1 2030 RELM-α+ interstitial macrophages inflammatory arthritis synovium SLC48A1 55652 RELM-α+ interstitial macrophages inflammatory arthritis synovium SLC9A3R2 9351 RELM-α+ interstitial macrophages inflammatory arthritis synovium SLCO2B1 11309 RELM-α+ interstitial macrophages inflammatory arthritis synovium SMAGP 57228 RELM-α+ interstitial macrophages inflammatory arthritis synovium SMIM10L1   1E+08 RELM-α+ interstitial macrophages inflammatory arthritis synovium SNX2 6643 RELM-α+ interstitial macrophages inflammatory arthritis synovium SNX3 8724 RELM-α+ interstitial macrophages inflammatory arthritis synovium SNX5 27131 RELM-α+ interstitial macrophages inflammatory arthritis synovium SNX6 58533 RELM-α+ interstitial macrophages inflammatory arthritis synovium SNX8 29886 RELM-α+ interstitial macrophages inflammatory arthritis synovium SPRED1 161742 RELM-α+ interstitial macrophages inflammatory arthritis synovium SPTBN1 6711 RELM-α+ interstitial macrophages inflammatory arthritis synovium SSH2 85464 RELM-α+ interstitial macrophages inflammatory arthritis synovium STAB1 23166 RELM-α+ interstitial macrophages inflammatory arthritis synovium STARD8 9754 RELM-α+ interstitial macrophages inflammatory arthritis synovium STK17B 9262 RELM-α+ interstitial macrophages inflammatory arthritis synovium SULF2 55959 RELM-α+ interstitial macrophages inflammatory arthritis synovium SULT1A1 6817 RELM-α+ interstitial macrophages inflammatory arthritis synovium TACC1 6867 RELM-α+ interstitial macrophages inflammatory arthritis synovium TCF4 6925 RELM-α+ interstitial macrophages inflammatory arthritis synovium TCN2 6948 RELM-α+ interstitial macrophages inflammatory arthritis synovium TEP1 7011 RELM-α+ interstitial macrophages inflammatory arthritis synovium TEX264 51368 RELM-α+ interstitial macrophages inflammatory arthritis synovium TF 7018 RELM-α+ interstitial macrophages inflammatory arthritis synovium TGFBR2 7048 RELM-α+ interstitial macrophages inflammatory arthritis synovium TIMD4 91937 RELM-α+ interstitial macrophages inflammatory arthritis synovium TIMP2 7077 RELM-α+ interstitial macrophages inflammatory arthritis synovium TLR7 51284 RELM-α+ interstitial macrophages inflammatory arthritis synovium TMEM106A 113277 RELM-α+ interstitial macrophages inflammatory arthritis synovium TMEM141 85014 RELM-α+ interstitial macrophages inflammatory arthritis synovium TMEM37 140738 RELM-α+ interstitial macrophages inflammatory arthritis synovium TMEM50A 23585 RELM-α+ interstitial macrophages inflammatory arthritis synovium TMEM59 9528 RELM-α+ interstitial macrophages inflammatory arthritis synovium TNFAIP8L2 79626 RELM-α+ interstitial macrophages inflammatory arthritis synovium TNFSF12 8742 RELM-α+ interstitial macrophages inflammatory arthritis synovium TNS1 7145 RELM-α+ interstitial macrophages inflammatory arthritis synovium TPPP3 51673 RELM-α+ interstitial macrophages inflammatory arthritis synovium TPRG1L 127262 RELM-α+ interstitial macrophages inflammatory arthritis synovium TRIM47 91107 RELM-α+ interstitial macrophages inflammatory arthritis synovium TRMT1 55621 RELM-α+ interstitial macrophages inflammatory arthritis synovium TSC22D3 1831 RELM-α+ interstitial macrophages inflammatory arthritis synovium TSEN34 79042 RELM-α+ interstitial macrophages inflammatory arthritis synovium TSLP 85480 RELM-α+ interstitial macrophages inflammatory arthritis synovium TSPAN17 26262 RELM-α+ interstitial macrophages inflammatory arthritis synovium TSPAN4 7106 RELM-α+ interstitial macrophages inflammatory arthritis synovium TXNIP 10628 RELM-α+ interstitial macrophages inflammatory arthritis synovium UNC93B1 81622 RELM-α+ interstitial macrophages inflammatory arthritis synovium VAT1 10493 RELM-α+ interstitial macrophages inflammatory arthritis synovium VKORC1 79001 RELM-α+ interstitial macrophages inflammatory arthritis synovium WWP1 11059 RELM-α+ interstitial macrophages inflammatory arthritis synovium YPEL3 83719 RELM-α+ interstitial macrophages inflammatory arthritis synovium ZBTB20 26137 RELM-α+ interstitial macrophages inflammatory arthritis synovium ZCCHC6 79670 RELM-α+ interstitial macrophages inflammatory arthritis synovium ALOX5 240 MHCII+ interstitial macrophages inflammatory arthritis synovium AP2A2 161 MHCII+ interstitial macrophages inflammatory arthritis synovium AQP1 358 MHCII+ interstitial macrophages inflammatory arthritis synovium ATF3 467 MHCII+ interstitial macrophages inflammatory arthritis synovium ATP2B1 490 MHCII+ interstitial macrophages inflammatory arthritis synovium CCL24 6369 MHCII+ interstitial macrophages inflammatory arthritis synovium CD163 9332 MHCII+ interstitial macrophages inflammatory arthritis synovium CD36 948 MHCII+ interstitial macrophages inflammatory arthritis synovium CD81 975 MHCII+ interstitial macrophages inflammatory arthritis synovium CD93 22918 MHCII+ interstitial macrophages inflammatory arthritis synovium CLEC10A 10462 MHCII+ interstitial macrophages inflammatory arthritis synovium CLEC12A 160364 MHCII+ interstitial macrophages inflammatory arthritis synovium CLTC 1213 MHCII+ interstitial macrophages inflammatory arthritis synovium DAB2 1601 MHCII+ interstitial macrophages inflammatory arthritis synovium DOK2 9046 MHCII+ interstitial macrophages inflammatory arthritis synovium DSE 29940 MHCII+ interstitial macrophages inflammatory arthritis synovium EGR1 1958 MHCII+ interstitial macrophages inflammatory arthritis synovium EHD4 30844 MHCII+ interstitial macrophages inflammatory arthritis synovium FOSB 2354 MHCII+ interstitial macrophages inflammatory arthritis synovium FRMD4B 23150 MHCII+ interstitial macrophages inflammatory arthritis synovium FXYD2 486 MHCII+ interstitial macrophages inflammatory arthritis synovium GAS7 8522 MHCII+ interstitial macrophages inflammatory arthritis synovium HLA-DQA1 3117 MHCII+ interstitial macrophages inflammatory arthritis synovium HLA-DQB1 3119 MHCII+ interstitial macrophages inflammatory arthritis synovium HLA-DRB5 3127 MHCII+ interstitial macrophages inflammatory arthritis synovium HSPA1A 3303 MHCII+ interstitial macrophages inflammatory arthritis synovium IER2 9592 MHCII+ interstitial macrophages inflammatory arthritis synovium IGF1 3479 MHCII+ interstitial macrophages inflammatory arthritis synovium IGFBP4 3487 MHCII+ interstitial macrophages inflammatory arthritis synovium IGHM 3507 MHCII+ interstitial macrophages inflammatory arthritis synovium IRF2BP2 359948 MHCII+ interstitial macrophages inflammatory arthritis synovium JUN 3725 MHCII+ interstitial macrophages inflammatory arthritis synovium JUND 3727 MHCII+ interstitial macrophages inflammatory arthritis synovium KLF2 10365 MHCII+ interstitial macrophages inflammatory arthritis synovium KLF4 9314 MHCII+ interstitial macrophages inflammatory arthritis synovium KLF6 1316 MHCII+ interstitial macrophages inflammatory arthritis synovium LIFR 3977 MHCII+ interstitial macrophages inflammatory arthritis synovium LPL 4023 MHCII+ interstitial macrophages inflammatory arthritis synovium LYZ 4069 MHCII+ interstitial macrophages inflammatory arthritis synovium MAF 4094 MHCII+ interstitial macrophages inflammatory arthritis synovium MAFB 9935 MHCII+ interstitial macrophages inflammatory arthritis synovium MALAT1 378938 MHCII+ interstitial macrophages inflammatory arthritis synovium MARCKSL1 65108 MHCII+ interstitial macrophages inflammatory arthritis synovium MEF2C 4208 MHCII+ interstitial macrophages inflammatory arthritis synovium METRNL 284207 MHCII+ interstitial macrophages inflammatory arthritis synovium MRC1 4360 MHCII+ interstitial macrophages inflammatory arthritis synovium MS4A7 58475 MHCII+ interstitial macrophages inflammatory arthritis synovium MT-CO1 4512 MHCII+ interstitial macrophages inflammatory arthritis synovium MT1A 4489 MHCII+ interstitial macrophages inflammatory arthritis synovium MT2A 4502 MHCII+ interstitial macrophages inflammatory arthritis synovium MTSS1 9788 MHCII+ interstitial macrophages inflammatory arthritis synovium NFKBIZ 64332 MHCII+ interstitial macrophages inflammatory arthritis synovium PF4 5196 MHCII+ interstitial macrophages inflammatory arthritis synovium PPP3CA 5530 MHCII+ interstitial macrophages inflammatory arthritis synovium RAB7B 338382 MHCII+ interstitial macrophages inflammatory arthritis synovium RBPJ 3516 MHCII+ interstitial macrophages inflammatory arthritis synovium RND3 390 MHCII+ interstitial macrophages inflammatory arthritis synovium RTN4 57142 MHCII+ interstitial macrophages inflammatory arthritis synovium SDC3 9672 MHCII+ interstitial macrophages inflammatory arthritis synovium SELENOP 6414 MHCII+ interstitial macrophages inflammatory arthritis synovium SERINC3 10955 MHCII+ interstitial macrophages inflammatory arthritis synovium SLAMF9 89886 MHCII+ interstitial macrophages inflammatory arthritis synovium SNX5 27131 MHCII+ interstitial macrophages inflammatory arthritis synovium TMEM176A 55365 MHCII+ interstitial macrophages inflammatory arthritis synovium TMEM176B 28959 MHCII+ interstitial macrophages inflammatory arthritis synovium TUBB2A 7280 MHCII+ interstitial macrophages inflammatory arthritis synovium TXNIP 10628 MHCII+ interstitial macrophages inflammatory arthritis synovium WNK1 65125 MHCII+ interstitial macrophages inflammatory arthritis synovium WWP1 11059 MHCII+ interstitial macrophages inflammatory arthritis synovium ZFP36L1 677 MHCII+ interstitial macrophages inflammatory arthritis synovium ACOT7 11332 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ACP5 54 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ACTR2 10097 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ADAM8 101 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ADSSL1 122622 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium AGPAT4 56895 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium AGPAT5 55326 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium AK2 204 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium AK6 1.02E+08 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ALDOA 226 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ANP32B 10541 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ANXA1 301 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ANXA2 302 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ANXA5 308 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium APEX1 328 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium APOBEC1 339 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium APRT 353 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ARF6 382 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATOX1 475 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATP5F1E 514 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATP5G1 516 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATP5G3 518 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATP5L 10632 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATP5ME 521 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATP5O 539 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATP6V0E1 8992 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATP6V1A 523 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATP6V1B2 526 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATP6V1C1 528 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATP6V1D 51382 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATP6V1E1 529 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATP6V1G1 9550 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ATPIF1 93974 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium AVPI1 60370 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium AZIN1 51582 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium B4GALT1 2683 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium BANF1 8815 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium BAX 581 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium BDH2 56898 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium BHLHE40 8553 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium BOLA2 552900 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium BTG1 694 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium C14orf2 9556 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium C1QBP 708 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium C6orf62 81688 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium C8orf59 401466 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CALM1 801 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CAV1 857 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CAV2 858 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CCT2 10576 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CCT3 7203 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CCT8 10694 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CD44 960 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CHCHD2 51142 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CHCHD4 131474 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CITED2 10370 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CKAP4 10970 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CLEC4D 338339 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CLEC4E 26253 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CLEC6A 93978 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium COPS9 150678 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium COX17 10063 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium COX5A 9377 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium COX6B1 1340 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium COX7A2 1347 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium COX7B 1349 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium COX7C 1350 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CSTB 1476 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CTSK 1513 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CTSV 1515 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CXCL16 58191 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CXCL3 2921 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium CYCS 54205 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium DDT 1652 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium DNAJC2 27000 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium DTYMK 1841 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EBNA1BP2 10969 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EEF1E1 9521 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EEF1G 1937 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EFHD2 79180 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EHD1 10938 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EIF1AY 9086 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EIF2S1 1965 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EIF2S2 8894 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EIF3J 8669 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EIF4A1 1973 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EIF4G2 1982 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EIF5A 1984 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EIF6 3692 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EMC6 83460 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ENO1 2023 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ERH 2079 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ESD 2098 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium EZR 7430 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium FABP5 2171 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium FAM129B 64855 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium FAM162A 26355 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium FBL 2091 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium FCF1 51077 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium FN1 2335 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium FURIN 5045 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium G3BP1 10146 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium GAPDH 2597 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium GCSH 2653 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium GLRX 2745 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium GNA13 10672 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium GNGT2 2793 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium GNL3 26354 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium GPR137B 7107 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium HDGF 3068 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium HIF1A 3091 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium HIGD1A 25994 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium HILPDA 29923 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium HNRNPA0 10949 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium HNRNPA1 3178 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium HNRNPAB 3182 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium HSP90AA1 3320 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium HSP90AB1 3326 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium HSPA9 3313 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium HSPD1 3329 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium HSPE1 3336 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ID2 3398 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium IFRD1 3475 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium IL1RN 3557 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium IMPDH2 3615 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ITGA5 3678 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ITGAV 3685 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium JARID2 3720 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium KCNN4 3783 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium LASP1 3927 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium LDHA 3939 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium LFNG 3955 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium LGALS1 3956 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium LGALS3 3958 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium LLPH 84298 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium LMNA 4000 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium LOC102724828 1.03E+08 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium LPL 4023 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium LSM7 51690 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium M6PR 4074 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MAGOH 4116 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MALT1 10892 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MAP4K4 9448 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MCL1 4170 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MDH2 4191 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MDM2 4193 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MIF 4282 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MMP14 4323 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MMP19 4327 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MRPL12 6182 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MRPL20 55052 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MRPL52 122704 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MRPL54 116541 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MRPS14 63931 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MRPS28 28957 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MRTO4 51154 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MS4A7 58475 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MT-ATP8 4509 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MT-CYB 4519 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MT-ND1 4535 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium MT-ND3 4537 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NAA50 80218 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NCEH1 57552 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NCL 4691 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NDUFAB1 4706 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NDUFB6 4712 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NDUFC1 4717 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NDUFC2 4718 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NDUFS6 4726 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NFATC1 4772 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NFKBIA 4792 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NHP2 55651 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NIP7 51388 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NME1 4830 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NOLC1 9221 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NOP10 55505 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NOP56 10528 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NOP58 51602 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NPM1 4869 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NPM3 10360 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NRP2 8828 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NSD2 7468 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NSUN2 54888 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NUDCD2 134492 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium NUS1 116150 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ODC1 4953 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium OSBPL8 114882 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PA2G4 5036 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PCBP1 5093 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PDPN 10630 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PFDN4 5203 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PFN1 5216 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PGAM1 5223 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PGK1 5230 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PHB2 11331 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PIK3R5 23533 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PKM 5315 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PLIN2 123 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PLXND1 23129 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PNO1 56902 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium POLR2K 5440 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium POLR2L 5441 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PPA1 5464 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PPP2CA 5515 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PRMT1 3276 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PSMA3 5684 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PSMA6 5687 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PSMB5 5693 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PSMB6 5694 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PSMB7 5695 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PSMD14 10213 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PTBP3 9991 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium PTMA 5757 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RACK1 10399 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RAI14 26064 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RALA 5898 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RAN 5901 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RANBP1 5902 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RBM3 5935 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RBX1 9978 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RGCC 28984 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RNF149 284996 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RNF19B 127544 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ROMO1 140823 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPL12 6136 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPL22 6146 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPL22L1 200916 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPL23 9349 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPL27 6155 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPL35 11224 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPL36A 6173 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPL36AL 6166 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPL37A 6168 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPL38 6169 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPL39 6170 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPL5 6125 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPLP1 6176 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPLP2 6181 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS10 6204 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS12 6206 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS15A 6210 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS17 6218 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS18 6222 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS19 6223 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS2 6187 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS21 6227 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS26 6231 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS27A 6233 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS27L 51065 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS3 6188 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS3A 6189 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium RPS8 6202 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium S100A10 6281 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium S100A11 6282 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium S100A4 6275 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SDC1 6382 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SDC4 6385 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SEC61B 10952 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SEMA4D 10507 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SERBP1 26135 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SET 6418 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SFPQ 6421 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SGK1 6446 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SLC37A2 219855 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SLC43A2 124935 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SLIRP 81892 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SMS 6611 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SNHG6 641638 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SNRPD1 6632 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SNRPD2 6633 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SNRPD3 6634 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SNRPE 6635 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SNRPF 6636 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SNU13 4809 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SOD1 6647 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SOD2 6648 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SPP1 6696 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SQSTM1 8878 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SRSF3 6428 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium SRSF7 6432 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TAF1D 79101 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TCIRG1 10312 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TCP1 6950 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TCTEX1D2 255758 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TIMM10 26519 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TIMM13 26517 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TIMM17A 10440 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TIMM8A 1678 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TIMP1 7076 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TNFAIP2 7127 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TNFAIP3 7128 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TOMM20 9804 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TOMM40 10452 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TOMM5 401505 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TPI1 7167 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TPM1 7168 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TPT1 7178 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TRAF1 7185 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TSC22D1 8848 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TUBA1C 84790 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TUBB4B 10383 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TUBB6 84617 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TXN 7295 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium TXNRD1 7296 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium U2AF1 7307 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium UBE2A 7319 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium UBE2L3 7332 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium UFM1 51569 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium UQCR10 29796 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium UQCR11 10975 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium UQCRB 7381 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium UQCRQ 27089 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium USMG5 84833 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium USP50 373509 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium VIM 7431 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium YBX1 4904 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium YBX3 8531 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium YWHAG 7532 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium YWHAZ 7534 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ZNF593 51042 CCR2+ARG1+ infiltrating macrophages inflammatory arthritis synovium ACOT7 11332 MHCII high dendritic cells inflammatory arthritis synovium ACTG1 71 MHCII high dendritic cells inflammatory arthritis synovium ASS1 445 MHCII high dendritic cells inflammatory arthritis synovium ATOX1 475 MHCII high dendritic cells inflammatory arthritis synovium ATP5F1 515 MHCII high dendritic cells inflammatory arthritis synovium AVPI1 60370 MHCII high dendritic cells inflammatory arthritis synovium B4GALNT1 2583 MHCII high dendritic cells inflammatory arthritis synovium BATF3 55509 MHCII high dendritic cells inflammatory arthritis synovium BCL2A1 597 MHCII high dendritic cells inflammatory arthritis synovium BHLHE40 8553 MHCII high dendritic cells inflammatory arthritis synovium BLOC1S2 282991 MHCII high dendritic cells inflammatory arthritis synovium BRI3BP 140707 MHCII high dendritic cells inflammatory arthritis synovium BTG2 7832 MHCII high dendritic cells inflammatory arthritis synovium C15orf48 84419 MHCII high dendritic cells inflammatory arthritis synovium C1orf21 81563 MHCII high dendritic cells inflammatory arthritis synovium C1orf54 79630 MHCII high dendritic cells inflammatory arthritis synovium CASP6 839 MHCII high dendritic cells inflammatory arthritis synovium CBFA2T3 863 MHCII high dendritic cells inflammatory arthritis synovium CCDC88A 55704 MHCII high dendritic cells inflammatory arthritis synovium CCND1 595 MHCII high dendritic cells inflammatory arthritis synovium CCND3 896 MHCII high dendritic cells inflammatory arthritis synovium CCR2 729230 MHCII high dendritic cells inflammatory arthritis synovium CD24 10013941 MHCII high dendritic cells inflammatory arthritis synovium CD47 961 MHCII high dendritic cells inflammatory arthritis synovium CD52 1043 MHCII high dendritic cells inflammatory arthritis synovium CD72 971 MHCII high dendritic cells inflammatory arthritis synovium CD74 972 MHCII high dendritic cells inflammatory arthritis synovium CD86 942 MHCII high dendritic cells inflammatory arthritis synovium CDKN2D 1032 MHCII high dendritic cells inflammatory arthritis synovium CFP 5199 MHCII high dendritic cells inflammatory arthritis synovium CKB 1152 MHCII high dendritic cells inflammatory arthritis synovium CLEC10A 10462 MHCII high dendritic cells inflammatory arthritis synovium CLEC6A 93978 MHCII high dendritic cells inflammatory arthritis synovium CNN2 1265 MHCII high dendritic cells inflammatory arthritis synovium CORO1A 11151 MHCII high dendritic cells inflammatory arthritis synovium CSF2RB 1439 MHCII high dendritic cells inflammatory arthritis synovium CSRNP1 64651 MHCII high dendritic cells inflammatory arthritis synovium CTSH 1512 MHCII high dendritic cells inflammatory arthritis synovium CXCL16 58191 MHCII high dendritic cells inflammatory arthritis synovium CYTIP 9595 MHCII high dendritic cells inflammatory arthritis synovium DAPP1 27071 MHCII high dendritic cells inflammatory arthritis synovium DBNL 28988 MHCII high dendritic cells inflammatory arthritis synovium DDOST 1650 MHCII high dendritic cells inflammatory arthritis synovium DENND4A 10260 MHCII high dendritic cells inflammatory arthritis synovium DPYSL2 1808 MHCII high dendritic cells inflammatory arthritis synovium EEF1B2 1933 MHCII high dendritic cells inflammatory arthritis synovium EEF1G 1937 MHCII high dendritic cells inflammatory arthritis synovium EIF3F 8665 MHCII high dendritic cells inflammatory arthritis synovium EMB 133418 MHCII high dendritic cells inflammatory arthritis synovium ETV3 2117 MHCII high dendritic cells inflammatory arthritis synovium EVA1B 55194 MHCII high dendritic cells inflammatory arthritis synovium FABP5 2171 MHCII high dendritic cells inflammatory arthritis synovium FAM129A 116496 MHCII high dendritic cells inflammatory arthritis synovium FBL 2091 MHCII high dendritic cells inflammatory arthritis synovium FDPS 2224 MHCII high dendritic cells inflammatory arthritis synovium FGL2 10875 MHCII high dendritic cells inflammatory arthritis synovium FGR 2268 MHCII high dendritic cells inflammatory arthritis synovium FH 2271 MHCII high dendritic cells inflammatory arthritis synovium GLIPR2 152007 MHCII high dendritic cells inflammatory arthritis synovium GM2A 2760 MHCII high dendritic cells inflammatory arthritis synovium GPR132 29933 MHCII high dendritic cells inflammatory arthritis synovium GPR171 29909 MHCII high dendritic cells inflammatory arthritis synovium GRK3 157 MHCII high dendritic cells inflammatory arthritis synovium H2AFY 9555 MHCII high dendritic cells inflammatory arthritis synovium H2AFZ 3015 MHCII high dendritic cells inflammatory arthritis synovium HLA-DMA 3108 MHCII high dendritic cells inflammatory arthritis synovium HLA-DMB 3109 MHCII high dendritic cells inflammatory arthritis synovium HLA-DQA1 3117 MHCII high dendritic cells inflammatory arthritis synovium HLA-DQB1 3119 MHCII high dendritic cells inflammatory arthritis synovium HLA-DRB5 3127 MHCII high dendritic cells inflammatory arthritis synovium HM13 81502 MHCII high dendritic cells inflammatory arthritis synovium HSD17B10 3028 MHCII high dendritic cells inflammatory arthritis synovium HSPA1A 3303 MHCII high dendritic cells inflammatory arthritis synovium ID2 3398 MHCII high dendritic cells inflammatory arthritis synovium IFITM2 10581 MHCII high dendritic cells inflammatory arthritis synovium IFNGR1 3459 MHCII high dendritic cells inflammatory arthritis synovium IL1B 3553 MHCII high dendritic cells inflammatory arthritis synovium IL1R2 7850 MHCII high dendritic cells inflammatory arthritis synovium IL2RG 3561 MHCII high dendritic cells inflammatory arthritis synovium ITGAX 3687 MHCII high dendritic cells inflammatory arthritis synovium ITGB7 3695 MHCII high dendritic cells inflammatory arthritis synovium JAK2 3717 MHCII high dendritic cells inflammatory arthritis synovium JAML 120425 MHCII high dendritic cells inflammatory arthritis synovium KIAA0040 9674 MHCII high dendritic cells inflammatory arthritis synovium KLRB1 3820 MHCII high dendritic cells inflammatory arthritis synovium KLRD1 3824 MHCII high dendritic cells inflammatory arthritis synovium LACTB 114294 MHCII high dendritic cells inflammatory arthritis synovium LIMD2 80774 MHCII high dendritic cells inflammatory arthritis synovium LMNB1 4001 MHCII high dendritic cells inflammatory arthritis synovium LMO4 8543 MHCII high dendritic cells inflammatory arthritis synovium LSP1 4046 MHCII high dendritic cells inflammatory arthritis synovium LSR 51599 MHCII high dendritic cells inflammatory arthritis synovium LTB4R 1241 MHCII high dendritic cells inflammatory arthritis synovium MARCKSL1 65108 MHCII high dendritic cells inflammatory arthritis synovium MED30 90390 MHCII high dendritic cells inflammatory arthritis synovium MPC1 51660 MHCII high dendritic cells inflammatory arthritis synovium MYD88 4615 MHCII high dendritic cells inflammatory arthritis synovium MYO1G 64005 MHCII high dendritic cells inflammatory arthritis synovium NAAA 27163 MHCII high dendritic cells inflammatory arthritis synovium NAGA 4668 MHCII high dendritic cells inflammatory arthritis synovium NAPSA 9476 MHCII high dendritic cells inflammatory arthritis synovium NDUFA6 4700 MHCII high dendritic cells inflammatory arthritis synovium NR4A2 4929 MHCII high dendritic cells inflammatory arthritis synovium OLFM1 10439 MHCII high dendritic cells inflammatory arthritis synovium PAK1 5058 MHCII high dendritic cells inflammatory arthritis synovium PDLIM1 9124 MHCII high dendritic cells inflammatory arthritis synovium PFKP 5214 MHCII high dendritic cells inflammatory arthritis synovium PIM1 5292 MHCII high dendritic cells inflammatory arthritis synovium PKIB 5570 MHCII high dendritic cells inflammatory arthritis synovium PLBD1 79887 MHCII high dendritic cells inflammatory arthritis synovium PLSCR1 5359 MHCII high dendritic cells inflammatory arthritis synovium PMVK 10654 MHCII high dendritic cells inflammatory arthritis synovium PRCP 5547 MHCII high dendritic cells inflammatory arthritis synovium PRKAR2A 5576 MHCII high dendritic cells inflammatory arthritis synovium PSMB8 5696 MHCII high dendritic cells inflammatory arthritis synovium PSMB9 5698 MHCII high dendritic cells inflammatory arthritis synovium PSME1 5720 MHCII high dendritic cells inflammatory arthritis synovium PTPRC 5788 MHCII high dendritic cells inflammatory arthritis synovium RAMP1 10267 MHCII high dendritic cells inflammatory arthritis synovium RARA 5914 MHCII high dendritic cells inflammatory arthritis synovium REL 5966 MHCII high dendritic cells inflammatory arthritis synovium RGS1 5996 MHCII high dendritic cells inflammatory arthritis synovium RIN3 79890 MHCII high dendritic cells inflammatory arthritis synovium ROGDI 79641 MHCII high dendritic cells inflammatory arthritis synovium RPL13 6137 MHCII high dendritic cells inflammatory arthritis synovium RPL14 9045 MHCII high dendritic cells inflammatory arthritis synovium RPL15 6138 MHCII high dendritic cells inflammatory arthritis synovium RPL17 6139 MHCII high dendritic cells inflammatory arthritis synovium RPL32 6161 MHCII high dendritic cells inflammatory arthritis synovium RPL39 6170 MHCII high dendritic cells inflammatory arthritis synovium RPL4 6124 MHCII high dendritic cells inflammatory arthritis synovium RPLP0 6175 MHCII high dendritic cells inflammatory arthritis synovium RPS11 6205 MHCII high dendritic cells inflammatory arthritis synovium RPS16 6217 MHCII high dendritic cells inflammatory arthritis synovium RPS18 6222 MHCII high dendritic cells inflammatory arthritis synovium RPS19 6223 MHCII high dendritic cells inflammatory arthritis synovium RPS4Y1 6192 MHCII high dendritic cells inflammatory arthritis synovium RPS6 6194 MHCII high dendritic cells inflammatory arthritis synovium RPS7 6201 MHCII high dendritic cells inflammatory arthritis synovium RPSA 3921 MHCII high dendritic cells inflammatory arthritis synovium S100A11 6282 MHCII high dendritic cells inflammatory arthritis synovium SCAND1 51282 MHCII high dendritic cells inflammatory arthritis synovium SDF2L1 23753 MHCII high dendritic cells inflammatory arthritis synovium SEC61B 10952 MHCII high dendritic cells inflammatory arthritis synovium SELPLG 6404 MHCII high dendritic cells inflammatory arthritis synovium SLAMF9 89886 MHCII high dendritic cells inflammatory arthritis synovium SPINT1 6692 MHCII high dendritic cells inflammatory arthritis synovium SRI 6717 MHCII high dendritic cells inflammatory arthritis synovium ST3GAL4 6484 MHCII high dendritic cells inflammatory arthritis synovium SUB1 10923 MHCII high dendritic cells inflammatory arthritis synovium SYNGR2 9144 MHCII high dendritic cells inflammatory arthritis synovium TAP1 6890 MHCII high dendritic cells inflammatory arthritis synovium TAX1BP3 30851 MHCII high dendritic cells inflammatory arthritis synovium TES 26136 MHCII high dendritic cells inflammatory arthritis synovium TIMP1 7076 MHCII high dendritic cells inflammatory arthritis synovium TMEM123 114908 MHCII high dendritic cells inflammatory arthritis synovium TMEM173 340061 MHCII high dendritic cells inflammatory arthritis synovium TMEM176A 55365 MHCII high dendritic cells inflammatory arthritis synovium TMEM176B 28959 MHCII high dendritic cells inflammatory arthritis synovium TMSB10 9168 MHCII high dendritic cells inflammatory arthritis synovium TNIP3 79931 MHCII high dendritic cells inflammatory arthritis synovium TRAF1 7185 MHCII high dendritic cells inflammatory arthritis synovium TRAPPC5 126003 MHCII high dendritic cells inflammatory arthritis synovium TSPAN13 27075 MHCII high dendritic cells inflammatory arthritis synovium TUBA1A 7846 MHCII high dendritic cells inflammatory arthritis synovium UNC119 9094 MHCII high dendritic cells inflammatory arthritis synovium UVRAG 7405 MHCII high dendritic cells inflammatory arthritis synovium VASP 7408 MHCII high dendritic cells inflammatory arthritis synovium VRK1 7443 MHCII high dendritic cells inflammatory arthritis synovium YWHAH 7533 MHCII high dendritic cells inflammatory arthritis synovium ZYX 7791 MHCII high dendritic cells inflammatory arthritis synovium ACOT7 11332 STMN1+ proliferating cells inflammatory arthritis synovium ACP5 54 STMN1+ proliferating cells inflammatory arthritis synovium ACTL6A 86 STMN1+ proliferating cells inflammatory arthritis synovium ACTN4 81 STMN1+ proliferating cells inflammatory arthritis synovium ADSS 159 STMN1+ proliferating cells inflammatory arthritis synovium AGPAT5 55326 STMN1+ proliferating cells inflammatory arthritis synovium AIMP2 7965 STMN1+ proliferating cells inflammatory arthritis synovium AK2 204 STMN1+ proliferating cells inflammatory arthritis synovium AK6 1.02E+08 STMN1+ proliferating cells inflammatory arthritis synovium ALYREF 10189 STMN1+ proliferating cells inflammatory arthritis synovium ANAPC11 51529 STMN1+ proliferating cells inflammatory arthritis synovium ANAPC5 51433 STMN1+ proliferating cells inflammatory arthritis synovium ANLN 54443 STMN1+ proliferating cells inflammatory arthritis synovium ANP32B 10541 STMN1+ proliferating cells inflammatory arthritis synovium ANP32E 81611 STMN1+ proliferating cells inflammatory arthritis synovium AP1S1 1174 STMN1+ proliferating cells inflammatory arthritis synovium APEX1 328 STMN1+ proliferating cells inflammatory arthritis synovium ARHGAP11A 9824 STMN1+ proliferating cells inflammatory arthritis synovium ARID1A 8289 STMN1+ proliferating cells inflammatory arthritis synovium ARL6IP1 23204 STMN1+ proliferating cells inflammatory arthritis synovium ARL8B 55207 STMN1+ proliferating cells inflammatory arthritis synovium ARPP19 10776 STMN1+ proliferating cells inflammatory arthritis synovium ASF1B 55723 STMN1+ proliferating cells inflammatory arthritis synovium ASPM 259266 STMN1+ proliferating cells inflammatory arthritis synovium ATAD2 29028 STMN1+ proliferating cells inflammatory arthritis synovium ATP5B 506 STMN1+ proliferating cells inflammatory arthritis synovium ATP5F1 515 STMN1+ proliferating cells inflammatory arthritis synovium ATP5G1 516 STMN1+ proliferating cells inflammatory arthritis synovium ATP5G2 517 STMN1+ proliferating cells inflammatory arthritis synovium ATP5G3 518 STMN1+ proliferating cells inflammatory arthritis synovium ATP5J2 9551 STMN1+ proliferating cells inflammatory arthritis synovium ATP5L 10632 STMN1+ proliferating cells inflammatory arthritis synovium ATP5ME 521 STMN1+ proliferating cells inflammatory arthritis synovium ATP5O 539 STMN1+ proliferating cells inflammatory arthritis synovium ATPIF1 93974 STMN1+ proliferating cells inflammatory arthritis synovium AURKA 6790 STMN1+ proliferating cells inflammatory arthritis synovium AURKB 9212 STMN1+ proliferating cells inflammatory arthritis synovium BAG1 573 STMN1+ proliferating cells inflammatory arthritis synovium BANF1 8815 STMN1+ proliferating cells inflammatory arthritis synovium BAZ1A 11177 STMN1+ proliferating cells inflammatory arthritis synovium BCKDK 10295 STMN1+ proliferating cells inflammatory arthritis synovium BDH2 56898 STMN1+ proliferating cells inflammatory arthritis synovium BEX3 27018 STMN1+ proliferating cells inflammatory arthritis synovium BICD2 23299 STMN1+ proliferating cells inflammatory arthritis synovium BIRC2 329 STMN1+ proliferating cells inflammatory arthritis synovium BIRC5 332 STMN1+ proliferating cells inflammatory arthritis synovium BOLA2 552900 STMN1+ proliferating cells inflammatory arthritis synovium BOLA3 388962 STMN1+ proliferating cells inflammatory arthritis synovium BRD7 29117 STMN1+ proliferating cells inflammatory arthritis synovium BRIX1 55299 STMN1+ proliferating cells inflammatory arthritis synovium BUB1 699 STMN1+ proliferating cells inflammatory arthritis synovium BUB1B 701 STMN1+ proliferating cells inflammatory arthritis synovium BUB3 9184 STMN1+ proliferating cells inflammatory arthritis synovium C11orf58 10944 STMN1+ proliferating cells inflammatory arthritis synovium C14orf2 9556 STMN1+ proliferating cells inflammatory arthritis synovium C1QBP 708 STMN1+ proliferating cells inflammatory arthritis synovium C20orf24 55969 STMN1+ proliferating cells inflammatory arthritis synovium C4ORF3 401152 STMN1+ proliferating cells inflammatory arthritis synovium C6orf62 81688 STMN1+ proliferating cells inflammatory arthritis synovium CACYBP 27101 STMN1+ proliferating cells inflammatory arthritis synovium CALM3 808 STMN1+ proliferating cells inflammatory arthritis synovium CAPRIN1 4076 STMN1+ proliferating cells inflammatory arthritis synovium CAV1 857 STMN1+ proliferating cells inflammatory arthritis synovium CAV2 858 STMN1+ proliferating cells inflammatory arthritis synovium CBFB 865 STMN1+ proliferating cells inflammatory arthritis synovium CBX1 10951 STMN1+ proliferating cells inflammatory arthritis synovium CBX3 11335 STMN1+ proliferating cells inflammatory arthritis synovium CBX5 23468 STMN1+ proliferating cells inflammatory arthritis synovium CCDC25 55246 STMN1+ proliferating cells inflammatory arthritis synovium CCDC34 91057 STMN1+ proliferating cells inflammatory arthritis synovium CCDC88A 55704 STMN1+ proliferating cells inflammatory arthritis synovium CCNA2 890 STMN1+ proliferating cells inflammatory arthritis synovium CCNB1 891 STMN1+ proliferating cells inflammatory arthritis synovium CCNB2 9133 STMN1+ proliferating cells inflammatory arthritis synovium CCND1 595 STMN1+ proliferating cells inflammatory arthritis synovium CCNE2 9134 STMN1+ proliferating cells inflammatory arthritis synovium CCT2 10576 STMN1+ proliferating cells inflammatory arthritis synovium CCT3 7203 STMN1+ proliferating cells inflammatory arthritis synovium CCT7 10574 STMN1+ proliferating cells inflammatory arthritis synovium CCT8 10694 STMN1+ proliferating cells inflammatory arthritis synovium CD44 960 STMN1+ proliferating cells inflammatory arthritis synovium CDC20 991 STMN1+ proliferating cells inflammatory arthritis synovium CDC45 8318 STMN1+ proliferating cells inflammatory arthritis synovium CDCA2 157313 STMN1+ proliferating cells inflammatory arthritis synovium CDCA3 83461 STMN1+ proliferating cells inflammatory arthritis synovium CDCA4 55038 STMN1+ proliferating cells inflammatory arthritis synovium CDCA8 55143 STMN1+ proliferating cells inflammatory arthritis synovium CDK1 983 STMN1+ proliferating cells inflammatory arthritis synovium CDK4 1019 STMN1+ proliferating cells inflammatory arthritis synovium CDKN2C 1031 STMN1+ proliferating cells inflammatory arthritis synovium CDKN2D 1032 STMN1+ proliferating cells inflammatory arthritis synovium CDKN3 1033 STMN1+ proliferating cells inflammatory arthritis synovium CENPA 1058 STMN1+ proliferating cells inflammatory arthritis synovium CENPE 1062 STMN1+ proliferating cells inflammatory arthritis synovium CENPF 1063 STMN1+ proliferating cells inflammatory arthritis synovium CENPH 64946 STMN1+ proliferating cells inflammatory arthritis synovium CENPK 64105 STMN1+ proliferating cells inflammatory arthritis synovium CENPM 79019 STMN1+ proliferating cells inflammatory arthritis synovium CENPQ 55166 STMN1+ proliferating cells inflammatory arthritis synovium CENPS 370708 STMN1+ proliferating cells inflammatory arthritis synovium CENPW 387103 STMN1+ proliferating cells inflammatory arthritis synovium CENPX 201254 STMN1+ proliferating cells inflammatory arthritis synovium CEP55 55165 STMN1+ proliferating cells inflammatory arthritis synovium CEP83 51134 STMN1+ proliferating cells inflammatory arthritis synovium CHCHD1 118487 STMN1+ proliferating cells inflammatory arthritis synovium CHCHD10 400916 STMN1+ proliferating cells inflammatory arthritis synovium CISD1 55847 STMN1+ proliferating cells inflammatory arthritis synovium CITED2 10370 STMN1+ proliferating cells inflammatory arthritis synovium CKAP2 26586 STMN1+ proliferating cells inflammatory arthritis synovium CKAP2L 150468 STMN1+ proliferating cells inflammatory arthritis synovium CKAP4 10970 STMN1+ proliferating cells inflammatory arthritis synovium CKAP5 9793 STMN1+ proliferating cells inflammatory arthritis synovium CKS1B 1163 STMN1+ proliferating cells inflammatory arthritis synovium CKS2 1164 STMN1+ proliferating cells inflammatory arthritis synovium CLIC4 25932 STMN1+ proliferating cells inflammatory arthritis synovium CLSPN 63967 STMN1+ proliferating cells inflammatory arthritis synovium CMC2 56942 STMN1+ proliferating cells inflammatory arthritis synovium CNIH4 29097 STMN1+ proliferating cells inflammatory arthritis synovium CNOT6 57472 STMN1+ proliferating cells inflammatory arthritis synovium COPS9 150678 STMN1+ proliferating cells inflammatory arthritis synovium COQ7 10229 STMN1+ proliferating cells inflammatory arthritis synovium COX20 116228 STMN1+ proliferating cells inflammatory arthritis synovium COX5A 9377 STMN1+ proliferating cells inflammatory arthritis synovium COX5B 1329 STMN1+ proliferating cells inflammatory arthritis synovium COX6C 1345 STMN1+ proliferating cells inflammatory arthritis synovium COX7A2 1347 STMN1+ proliferating cells inflammatory arthritis synovium COX7C 1350 STMN1+ proliferating cells inflammatory arthritis synovium CPSF2 53981 STMN1+ proliferating cells inflammatory arthritis synovium CRIP2 1397 STMN1+ proliferating cells inflammatory arthritis synovium CSRP1 1465 STMN1+ proliferating cells inflammatory arthritis synovium CTCF 10664 STMN1+ proliferating cells inflammatory arthritis synovium CTNNB1 1499 STMN1+ proliferating cells inflammatory arthritis synovium CTSK 1513 STMN1+ proliferating cells inflammatory arthritis synovium CYB5R3 1727 STMN1+ proliferating cells inflammatory arthritis synovium CYC1 1537 STMN1+ proliferating cells inflammatory arthritis synovium CYCS 54205 STMN1+ proliferating cells inflammatory arthritis synovium DAZAP1 26528 STMN1+ proliferating cells inflammatory arthritis synovium DBF4 10926 STMN1+ proliferating cells inflammatory arthritis synovium DCK 1633 STMN1+ proliferating cells inflammatory arthritis synovium DCTPP1 79077 STMN1+ proliferating cells inflammatory arthritis synovium DCUN1D5 84259 STMN1+ proliferating cells inflammatory arthritis synovium DDT 1652 STMN1+ proliferating cells inflammatory arthritis synovium DDX18 8886 STMN1+ proliferating cells inflammatory arthritis synovium DDX21 9188 STMN1+ proliferating cells inflammatory arthritis synovium DDX39A 10212 STMN1+ proliferating cells inflammatory arthritis synovium DDX39B 7919 STMN1+ proliferating cells inflammatory arthritis synovium DEK 7913 STMN1+ proliferating cells inflammatory arthritis synovium DENR 8562 STMN1+ proliferating cells inflammatory arthritis synovium DHFR 1719 STMN1+ proliferating cells inflammatory arthritis synovium DHX15 1665 STMN1+ proliferating cells inflammatory arthritis synovium DHX9 1660 STMN1+ proliferating cells inflammatory arthritis synovium DIAPH3 81624 STMN1+ proliferating cells inflammatory arthritis synovium DKC1 1736 STMN1+ proliferating cells inflammatory arthritis synovium DLGAP5 9787 STMN1+ proliferating cells inflammatory arthritis synovium DNAJC2 27000 STMN1+ proliferating cells inflammatory arthritis synovium DNAJC9 23234 STMN1+ proliferating cells inflammatory arthritis synovium DNMT1 1786 STMN1+ proliferating cells inflammatory arthritis synovium DNPH1 10591 STMN1+ proliferating cells inflammatory arthritis synovium DPY30 84661 STMN1+ proliferating cells inflammatory arthritis synovium DTYMK 1841 STMN1+ proliferating cells inflammatory arthritis synovium DUT 1854 STMN1+ proliferating cells inflammatory arthritis synovium DYNLL2 140735 STMN1+ proliferating cells inflammatory arthritis synovium DYNLT1 6993 STMN1+ proliferating cells inflammatory arthritis synovium EEF1B2 1933 STMN1+ proliferating cells inflammatory arthritis synovium EEF1D 1936 STMN1+ proliferating cells inflammatory arthritis synovium EEF1E1 9521 STMN1+ proliferating cells inflammatory arthritis synovium EEF1G 1937 STMN1+ proliferating cells inflammatory arthritis synovium EIF1AD 84285 STMN1+ proliferating cells inflammatory arthritis synovium EIF1AY 9086 STMN1+ proliferating cells inflammatory arthritis synovium EIF2S2 8894 STMN1+ proliferating cells inflammatory arthritis synovium EIF3A 8661 STMN1+ proliferating cells inflammatory arthritis synovium EIF3C 8663 STMN1+ proliferating cells inflammatory arthritis synovium EIF3J 8669 STMN1+ proliferating cells inflammatory arthritis synovium EIF4G2 1982 STMN1+ proliferating cells inflammatory arthritis synovium EIF5A 1984 STMN1+ proliferating cells inflammatory arthritis synovium EIF6 3692 STMN1+ proliferating cells inflammatory arthritis synovium ELAVL1 1994 STMN1+ proliferating cells inflammatory arthritis synovium ELOC 6921 STMN1+ proliferating cells inflammatory arthritis synovium EMG1 10436 STMN1+ proliferating cells inflammatory arthritis synovium ENY2 56943 STMN1+ proliferating cells inflammatory arthritis synovium ERH 2079 STMN1+ proliferating cells inflammatory arthritis synovium ERI1 90459 STMN1+ proliferating cells inflammatory arthritis synovium ESCO2 157570 STMN1+ proliferating cells inflammatory arthritis synovium ETFB 2109 STMN1+ proliferating cells inflammatory arthritis synovium EXOSC8 11340 STMN1+ proliferating cells inflammatory arthritis synovium EZH2 2146 STMN1+ proliferating cells inflammatory arthritis synovium FABP5 2171 STMN1+ proliferating cells inflammatory arthritis synovium FAM111A 63901 STMN1+ proliferating cells inflammatory arthritis synovium FAM133B 257415 STMN1+ proliferating cells inflammatory arthritis synovium FBL 2091 STMN1+ proliferating cells inflammatory arthritis synovium FBXO5 26271 STMN1+ proliferating cells inflammatory arthritis synovium FEN1 2237 STMN1+ proliferating cells inflammatory arthritis synovium FIGNL1 63979 STMN1+ proliferating cells inflammatory arthritis synovium FKBP2 2286 STMN1+ proliferating cells inflammatory arthritis synovium FKBP3 2287 STMN1+ proliferating cells inflammatory arthritis synovium FKBP4 2288 STMN1+ proliferating cells inflammatory arthritis synovium FUS 2521 STMN1+ proliferating cells inflammatory arthritis synovium FXN 2395 STMN1+ proliferating cells inflammatory arthritis synovium G3BP1 10146 STMN1+ proliferating cells inflammatory arthritis synovium GADD45GIP1 90480 STMN1+ proliferating cells inflammatory arthritis synovium GAR1 54433 STMN1+ proliferating cells inflammatory arthritis synovium GAS2L3 283431 STMN1+ proliferating cells inflammatory arthritis synovium GATM 2628 STMN1+ proliferating cells inflammatory arthritis synovium GEMIN6 79833 STMN1+ proliferating cells inflammatory arthritis synovium GINS2 51659 STMN1+ proliferating cells inflammatory arthritis synovium GJA1 2697 STMN1+ proliferating cells inflammatory arthritis synovium GLIPR1 11010 STMN1+ proliferating cells inflammatory arthritis synovium GMNN 51053 STMN1+ proliferating cells inflammatory arthritis synovium GNL3 26354 STMN1+ proliferating cells inflammatory arthritis synovium GSPT1 2935 STMN1+ proliferating cells inflammatory arthritis synovium GTF2H5 404672 STMN1+ proliferating cells inflammatory arthritis synovium H1-4 3008 STMN1+ proliferating cells inflammatory arthritis synovium H1-5 3009 STMN1+ proliferating cells inflammatory arthritis synovium H2AFV 94239 STMN1+ proliferating cells inflammatory arthritis synovium H2AFX 3014 STMN1+ proliferating cells inflammatory arthritis synovium H2AFY 9555 STMN1+ proliferating cells inflammatory arthritis synovium H2AFZ 3015 STMN1+ proliferating cells inflammatory arthritis synovium HACD1 9200 STMN1+ proliferating cells inflammatory arthritis synovium HAT1 8520 STMN1+ proliferating cells inflammatory arthritis synovium HAUS1 115106 STMN1+ proliferating cells inflammatory arthritis synovium HAUS4 54930 STMN1+ proliferating cells inflammatory arthritis synovium HDAC2 3066 STMN1+ proliferating cells inflammatory arthritis synovium HDGF 3068 STMN1+ proliferating cells inflammatory arthritis synovium HELLS 3070 STMN1+ proliferating cells inflammatory arthritis synovium HINT1 3094 STMN1+ proliferating cells inflammatory arthritis synovium HIRIP3 8479 STMN1+ proliferating cells inflammatory arthritis synovium HIST1H1D 3007 STMN1+ proliferating cells inflammatory arthritis synovium HIST1H2AL 8332 STMN1+ proliferating cells inflammatory arthritis synovium HIST1H4A 8359 STMN1+ proliferating cells inflammatory arthritis synovium HIST2H2AC 8338 STMN1+ proliferating cells inflammatory arthritis synovium HJURP 55355 STMN1+ proliferating cells inflammatory arthritis synovium HMGB1 3146 STMN1+ proliferating cells inflammatory arthritis synovium HMGB2 3148 STMN1+ proliferating cells inflammatory arthritis synovium HMGB3 3149 STMN1+ proliferating cells inflammatory arthritis synovium HMGN1 3150 STMN1+ proliferating cells inflammatory arthritis synovium HMGN2 3151 STMN1+ proliferating cells inflammatory arthritis synovium HMGN5 79366 STMN1+ proliferating cells inflammatory arthritis synovium HMMR 3161 STMN1+ proliferating cells inflammatory arthritis synovium HNRNPA0 10949 STMN1+ proliferating cells inflammatory arthritis synovium HNRNPA1 3178 STMN1+ proliferating cells inflammatory arthritis synovium HNRNPA2B1 3181 STMN1+ proliferating cells inflammatory arthritis synovium HNRNPA3 220988 STMN1+ proliferating cells inflammatory arthritis synovium HNRNPAB 3182 STMN1+ proliferating cells inflammatory arthritis synovium HNRNPD 3184 STMN1+ proliferating cells inflammatory arthritis synovium HNRNPM 4670 STMN1+ proliferating cells inflammatory arthritis synovium HNRNPU 3192 STMN1+ proliferating cells inflammatory arthritis synovium HP1BP3 50809 STMN1+ proliferating cells inflammatory arthritis synovium HPF1 54969 STMN1+ proliferating cells inflammatory arthritis synovium HSP90AA1 3320 STMN1+ proliferating cells inflammatory arthritis synovium HSP90AB1 3326 STMN1+ proliferating cells inflammatory arthritis synovium HSP90B1 7184 STMN1+ proliferating cells inflammatory arthritis synovium HSPA14 51182 STMN1+ proliferating cells inflammatory arthritis synovium HSPA9 3313 STMN1+ proliferating cells inflammatory arthritis synovium HSPD1 3329 STMN1+ proliferating cells inflammatory arthritis synovium HSPE1 3336 STMN1+ proliferating cells inflammatory arthritis synovium HUWE1 10075 STMN1+ proliferating cells inflammatory arthritis synovium IDH3A 3419 STMN1+ proliferating cells inflammatory arthritis synovium ILF2 3608 STMN1+ proliferating cells inflammatory arthritis synovium ILF3 3609 STMN1+ proliferating cells inflammatory arthritis synovium IMMT 10989 STMN1+ proliferating cells inflammatory arthritis synovium IMPDH2 3615 STMN1+ proliferating cells inflammatory arthritis synovium INCENP 3619 STMN1+ proliferating cells inflammatory arthritis synovium ING1 3621 STMN1+ proliferating cells inflammatory arthritis synovium IPO5 3843 STMN1+ proliferating cells inflammatory arthritis synovium ITGAV 3685 STMN1+ proliferating cells inflammatory arthritis synovium ITPA 3704 STMN1+ proliferating cells inflammatory arthritis synovium IVNS1ABP 10625 STMN1+ proliferating cells inflammatory arthritis synovium JPT1 51155 STMN1+ proliferating cells inflammatory arthritis synovium KDELR2 11014 STMN1+ proliferating cells inflammatory arthritis synovium KHSRP 8570 STMN1+ proliferating cells inflammatory arthritis synovium KIAA1524 57650 STMN1+ proliferating cells inflammatory arthritis synovium KIF11 3832 STMN1+ proliferating cells inflammatory arthritis synovium KIF15 56992 STMN1+ proliferating cells inflammatory arthritis synovium KIF20A 10112 STMN1+ proliferating cells inflammatory arthritis synovium KIF20B 9585 STMN1+ proliferating cells inflammatory arthritis synovium KIF22 3835 STMN1+ proliferating cells inflammatory arthritis synovium KIF23 9493 STMN1+ proliferating cells inflammatory arthritis synovium KIF4A 24137 STMN1+ proliferating cells inflammatory arthritis synovium KIFC1 3833 STMN1+ proliferating cells inflammatory arthritis synovium KLHL5 51088 STMN1+ proliferating cells inflammatory arthritis synovium KMT5A 387893 STMN1+ proliferating cells inflammatory arthritis synovium KNL1 57082 STMN1+ proliferating cells inflammatory arthritis synovium KNSTRN 90417 STMN1+ proliferating cells inflammatory arthritis synovium KPNA2 3838 STMN1+ proliferating cells inflammatory arthritis synovium KPNA3 3839 STMN1+ proliferating cells inflammatory arthritis synovium KPNB1 3837 STMN1+ proliferating cells inflammatory arthritis synovium KTN1 3895 STMN1+ proliferating cells inflammatory arthritis synovium LARP7 51574 STMN1+ proliferating cells inflammatory arthritis synovium LARS 51520 STMN1+ proliferating cells inflammatory arthritis synovium LBR 3930 STMN1+ proliferating cells inflammatory arthritis synovium LDHA 3939 STMN1+ proliferating cells inflammatory arthritis synovium LIG1 3978 STMN1+ proliferating cells inflammatory arthritis synovium LMF2 91289 STMN1+ proliferating cells inflammatory arthritis synovium LMNA 4000 STMN1+ proliferating cells inflammatory arthritis synovium LMO4 8543 STMN1+ proliferating cells inflammatory arthritis synovium LPL 4023 STMN1+ proliferating cells inflammatory arthritis synovium LRPPRC 10128 STMN1+ proliferating cells inflammatory arthritis synovium LRR1 122769 STMN1+ proliferating cells inflammatory arthritis synovium LSM2 57819 STMN1+ proliferating cells inflammatory arthritis synovium LSM3 27258 STMN1+ proliferating cells inflammatory arthritis synovium LSM4 25804 STMN1+ proliferating cells inflammatory arthritis synovium LSM5 23658 STMN1+ proliferating cells inflammatory arthritis synovium LSM6 11157 STMN1+ proliferating cells inflammatory arthritis synovium LSM7 51690 STMN1+ proliferating cells inflammatory arthritis synovium LSM8 51691 STMN1+ proliferating cells inflammatory arthritis synovium LUC7L3 51747 STMN1+ proliferating cells inflammatory arthritis synovium LYAR 55646 STMN1+ proliferating cells inflammatory arthritis synovium M6PR 4074 STMN1+ proliferating cells inflammatory arthritis synovium MAD2L1 4085 STMN1+ proliferating cells inflammatory arthritis synovium MAGOH 4116 STMN1+ proliferating cells inflammatory arthritis synovium MAGOHB 55110 STMN1+ proliferating cells inflammatory arthritis synovium MAP4K4 9448 STMN1+ proliferating cells inflammatory arthritis synovium MAPK1 5594 STMN1+ proliferating cells inflammatory arthritis synovium MATR3 9782 STMN1+ proliferating cells inflammatory arthritis synovium MBD3 53615 STMN1+ proliferating cells inflammatory arthritis synovium MCM3 4172 STMN1+ proliferating cells inflammatory arthritis synovium MCM4 4173 STMN1+ proliferating cells inflammatory arthritis synovium MCM5 4174 STMN1+ proliferating cells inflammatory arthritis synovium MCM6 4175 STMN1+ proliferating cells inflammatory arthritis synovium MCM7 4176 STMN1+ proliferating cells inflammatory arthritis synovium MDH2 4191 STMN1+ proliferating cells inflammatory arthritis synovium MED30 90390 STMN1+ proliferating cells inflammatory arthritis synovium MELK 9833 STMN1+ proliferating cells inflammatory arthritis synovium METAP2 10988 STMN1+ proliferating cells inflammatory arthritis synovium MIF 4282 STMN1+ proliferating cells inflammatory arthritis synovium MINOS1 440574 STMN1+ proliferating cells inflammatory arthritis synovium MIS12 79003 STMN1+ proliferating cells inflammatory arthritis synovium MIS18A 54069 STMN1+ proliferating cells inflammatory arthritis synovium MIS18BP1 55320 STMN1+ proliferating cells inflammatory arthritis synovium MKI67 4288 STMN1+ proliferating cells inflammatory arthritis synovium MMP14 4323 STMN1+ proliferating cells inflammatory arthritis synovium MPHOSPH6 10200 STMN1+ proliferating cells inflammatory arthritis synovium MRPL12 6182 STMN1+ proliferating cells inflammatory arthritis synovium MRPL15 29088 STMN1+ proliferating cells inflammatory arthritis synovium MRPL18 29074 STMN1+ proliferating cells inflammatory arthritis synovium MRPL28 10573 STMN1+ proliferating cells inflammatory arthritis synovium MRPL34 64981 STMN1+ proliferating cells inflammatory arthritis synovium MRPL42 28977 STMN1+ proliferating cells inflammatory arthritis synovium MRPL49 740 STMN1+ proliferating cells inflammatory arthritis synovium MRPL51 51258 STMN1+ proliferating cells inflammatory arthritis synovium MRPL52 122704 STMN1+ proliferating cells inflammatory arthritis synovium MRPL57 78988 STMN1+ proliferating cells inflammatory arthritis synovium MRPS14 63931 STMN1+ proliferating cells inflammatory arthritis synovium MRPS17 51373 STMN1+ proliferating cells inflammatory arthritis synovium MRPS25 64432 STMN1+ proliferating cells inflammatory arthritis synovium MRPS26 64949 STMN1+ proliferating cells inflammatory arthritis synovium MRPS28 28957 STMN1+ proliferating cells inflammatory arthritis synovium MRPS36 92259 STMN1+ proliferating cells inflammatory arthritis synovium MT-ATP6 4508 STMN1+ proliferating cells inflammatory arthritis synovium MT-ATP8 4509 STMN1+ proliferating cells inflammatory arthritis synovium MT-CO1 4512 STMN1+ proliferating cells inflammatory arthritis synovium MT-CO2 4513 STMN1+ proliferating cells inflammatory arthritis synovium MT-CO3 4514 STMN1+ proliferating cells inflammatory arthritis synovium MT-ND1 4535 STMN1+ proliferating cells inflammatory arthritis synovium MT-ND3 4537 STMN1+ proliferating cells inflammatory arthritis synovium MT-ND4L 4539 STMN1+ proliferating cells inflammatory arthritis synovium MT1A 4489 STMN1+ proliferating cells inflammatory arthritis synovium MT2A 4502 STMN1+ proliferating cells inflammatory arthritis synovium MXD3 83463 STMN1+ proliferating cells inflammatory arthritis synovium MYADM 91663 STMN1+ proliferating cells inflammatory arthritis synovium MYBBP1A 10514 STMN1+ proliferating cells inflammatory arthritis synovium MYBL2 4605 STMN1+ proliferating cells inflammatory arthritis synovium MYCBP 26292 STMN1+ proliferating cells inflammatory arthritis synovium MYEF2 50804 STMN1+ proliferating cells inflammatory arthritis synovium NAA10 8260 STMN1+ proliferating cells inflammatory arthritis synovium NAA50 80218 STMN1+ proliferating cells inflammatory arthritis synovium NANS 54187 STMN1+ proliferating cells inflammatory arthritis synovium NAP1L1 4673 STMN1+ proliferating cells inflammatory arthritis synovium NASP 4678 STMN1+ proliferating cells inflammatory arthritis synovium NAV2 89797 STMN1+ proliferating cells inflammatory arthritis synovium NCAPD2 9918 STMN1+ proliferating cells inflammatory arthritis synovium NCAPD3 23310 STMN1+ proliferating cells inflammatory arthritis synovium NCAPG 64151 STMN1+ proliferating cells inflammatory arthritis synovium NCAPG2 54892 STMN1+ proliferating cells inflammatory arthritis synovium NCAPH 23397 STMN1+ proliferating cells inflammatory arthritis synovium NCAPH2 29781 STMN1+ proliferating cells inflammatory arthritis synovium NCBP1 4686 STMN1+ proliferating cells inflammatory arthritis synovium NCL 4691 STMN1+ proliferating cells inflammatory arthritis synovium NDC80 10403 STMN1+ proliferating cells inflammatory arthritis synovium NDUFA12 55967 STMN1+ proliferating cells inflammatory arthritis synovium NDUFA2 4695 STMN1+ proliferating cells inflammatory arthritis synovium NDUFA5 4698 STMN1+ proliferating cells inflammatory arthritis synovium NDUFAB1 4706 STMN1+ proliferating cells inflammatory arthritis synovium NDUFAF2 91942 STMN1+ proliferating cells inflammatory arthritis synovium NDUFAF4 29078 STMN1+ proliferating cells inflammatory arthritis synovium NDUFB10 4716 STMN1+ proliferating cells inflammatory arthritis synovium NDUFB11 54539 STMN1+ proliferating cells inflammatory arthritis synovium NDUFB6 4712 STMN1+ proliferating cells inflammatory arthritis synovium NDUFB7 4713 STMN1+ proliferating cells inflammatory arthritis synovium NDUFB8 4714 STMN1+ proliferating cells inflammatory arthritis synovium NDUFC1 4717 STMN1+ proliferating cells inflammatory arthritis synovium NDUFC2 4718 STMN1+ proliferating cells inflammatory arthritis synovium NDUFS5 4725 STMN1+ proliferating cells inflammatory arthritis synovium NDUFV2 4729 STMN1+ proliferating cells inflammatory arthritis synovium NFATC1 4772 STMN1+ proliferating cells inflammatory arthritis synovium NHP2 55651 STMN1+ proliferating cells inflammatory arthritis synovium NME1 4830 STMN1+ proliferating cells inflammatory arthritis synovium NMRAL1 57407 STMN1+ proliferating cells inflammatory arthritis synovium NMT2 9397 STMN1+ proliferating cells inflammatory arthritis synovium NOL7 51406 STMN1+ proliferating cells inflammatory arthritis synovium NOLC1 9221 STMN1+ proliferating cells inflammatory arthritis synovium NONO 4841 STMN1+ proliferating cells inflammatory arthritis synovium NOP10 55505 STMN1+ proliferating cells inflammatory arthritis synovium NOP16 51491 STMN1+ proliferating cells inflammatory arthritis synovium NOP56 10528 STMN1+ proliferating cells inflammatory arthritis synovium NOP58 51602 STMN1+ proliferating cells inflammatory arthritis synovium NPM1 4869 STMN1+ proliferating cells inflammatory arthritis synovium NPM3 10360 STMN1+ proliferating cells inflammatory arthritis synovium NRM 11270 STMN1+ proliferating cells inflammatory arthritis synovium NRP2 8828 STMN1+ proliferating cells inflammatory arthritis synovium NSD2 7468 STMN1+ proliferating cells inflammatory arthritis synovium NSMCE1 197370 STMN1+ proliferating cells inflammatory arthritis synovium NSUN2 54888 STMN1+ proliferating cells inflammatory arthritis synovium NUBP1 4682 STMN1+ proliferating cells inflammatory arthritis synovium NUCKS1 64710 STMN1+ proliferating cells inflammatory arthritis synovium NUDC 10726 STMN1+ proliferating cells inflammatory arthritis synovium NUDCD2 134492 STMN1+ proliferating cells inflammatory arthritis synovium NUDT5 11164 STMN1+ proliferating cells inflammatory arthritis synovium NUF2 83540 STMN1+ proliferating cells inflammatory arthritis synovium NUMA1 4926 STMN1+ proliferating cells inflammatory arthritis synovium NUP35 129401 STMN1+ proliferating cells inflammatory arthritis synovium NUP85 79902 STMN1+ proliferating cells inflammatory arthritis synovium NUP93 9688 STMN1+ proliferating cells inflammatory arthritis synovium NUSAP1 51203 STMN1+ proliferating cells inflammatory arthritis synovium NXT1 29107 STMN1+ proliferating cells inflammatory arthritis synovium ODC1 4953 STMN1+ proliferating cells inflammatory arthritis synovium ODF2 4957 STMN1+ proliferating cells inflammatory arthritis synovium OLA1 29789 STMN1+ proliferating cells inflammatory arthritis synovium ORC6 23594 STMN1+ proliferating cells inflammatory arthritis synovium OXCT1 5019 STMN1+ proliferating cells inflammatory arthritis synovium PA2G4 5036 STMN1+ proliferating cells inflammatory arthritis synovium PABPC1 26986 STMN1+ proliferating cells inflammatory arthritis synovium PABPC4 8761 STMN1+ proliferating cells inflammatory arthritis synovium PAICS 10606 STMN1+ proliferating cells inflammatory arthritis synovium PARK7 11315 STMN1+ proliferating cells inflammatory arthritis synovium PARL 55486 STMN1+ proliferating cells inflammatory arthritis synovium PBK 55872 STMN1+ proliferating cells inflammatory arthritis synovium PBRM1 55193 STMN1+ proliferating cells inflammatory arthritis synovium PCBD2 84105 STMN1+ proliferating cells inflammatory arthritis synovium PCBP1 5093 STMN1+ proliferating cells inflammatory arthritis synovium PCBP2 5094 STMN1+ proliferating cells inflammatory arthritis synovium PCLAF 9768 STMN1+ proliferating cells inflammatory arthritis synovium PCNA 5111 STMN1+ proliferating cells inflammatory arthritis synovium PDAP1 11333 STMN1+ proliferating cells inflammatory arthritis synovium PDCD5 9141 STMN1+ proliferating cells inflammatory arthritis synovium PDPK1 5170 STMN1+ proliferating cells inflammatory arthritis synovium PDS5A 23244 STMN1+ proliferating cells inflammatory arthritis synovium PFDN4 5203 STMN1+ proliferating cells inflammatory arthritis synovium PFDN6 10471 STMN1+ proliferating cells inflammatory arthritis synovium PGK1 5230 STMN1+ proliferating cells inflammatory arthritis synovium PGP 283871 STMN1+ proliferating cells inflammatory arthritis synovium PHB2 11331 STMN1+ proliferating cells inflammatory arthritis synovium PIH1D1 55011 STMN1+ proliferating cells inflammatory arthritis synovium PIMREG 54478 STMN1+ proliferating cells inflammatory arthritis synovium PKMYT1 9088 STMN1+ proliferating cells inflammatory arthritis synovium PLK1 5347 STMN1+ proliferating cells inflammatory arthritis synovium PLK4 10733 STMN1+ proliferating cells inflammatory arthritis synovium PLP2 5355 STMN1+ proliferating cells inflammatory arthritis synovium PMF1 11243 STMN1+ proliferating cells inflammatory arthritis synovium PNN 5411 STMN1+ proliferating cells inflammatory arthritis synovium POLD2 5425 STMN1+ proliferating cells inflammatory arthritis synovium POLE3 54107 STMN1+ proliferating cells inflammatory arthritis synovium POLE4 56655 STMN1+ proliferating cells inflammatory arthritis synovium POLR2A 5430 STMN1+ proliferating cells inflammatory arthritis synovium POLR2F 5435 STMN1+ proliferating cells inflammatory arthritis synovium POLR2L 5441 STMN1+ proliferating cells inflammatory arthritis synovium PPA1 5464 STMN1+ proliferating cells inflammatory arthritis synovium PPIA 5478 STMN1+ proliferating cells inflammatory arthritis synovium PPID 5481 STMN1+ proliferating cells inflammatory arthritis synovium PPIH 10465 STMN1+ proliferating cells inflammatory arthritis synovium PPP2R5C 5527 STMN1+ proliferating cells inflammatory arthritis synovium PRC1 9055 STMN1+ proliferating cells inflammatory arthritis synovium PRDX4 10549 STMN1+ proliferating cells inflammatory arthritis synovium PRIM1 5557 STMN1+ proliferating cells inflammatory arthritis synovium PRKAR2A 5576 STMN1+ proliferating cells inflammatory arthritis synovium PRMT1 3276 STMN1+ proliferating cells inflammatory arthritis synovium PRR11 55771 STMN1+ proliferating cells inflammatory arthritis synovium PRRC2A 7916 STMN1+ proliferating cells inflammatory arthritis synovium PSAT1 29968 STMN1+ proliferating cells inflammatory arthritis synovium PSIP1 11168 STMN1+ proliferating cells inflammatory arthritis synovium PSMA6 5687 STMN1+ proliferating cells inflammatory arthritis synovium PSMB7 5695 STMN1+ proliferating cells inflammatory arthritis synovium PSMC3 5702 STMN1+ proliferating cells inflammatory arthritis synovium PSMD1 5707 STMN1+ proliferating cells inflammatory arthritis synovium PSMD10 5716 STMN1+ proliferating cells inflammatory arthritis synovium PSMD14 10213 STMN1+ proliferating cells inflammatory arthritis synovium PSMG2 56984 STMN1+ proliferating cells inflammatory arthritis synovium PTBP1 5725 STMN1+ proliferating cells inflammatory arthritis synovium PTGES3 10728 STMN1+ proliferating cells inflammatory arthritis synovium PTMA 5757 STMN1+ proliferating cells inflammatory arthritis synovium PTPN7 5778 STMN1+ proliferating cells inflammatory arthritis synovium PURB 5814 STMN1+ proliferating cells inflammatory arthritis synovium QDPR 5860 STMN1+ proliferating cells inflammatory arthritis synovium RACGAP1 29127 STMN1+ proliferating cells inflammatory arthritis synovium RACK1 10399 STMN1+ proliferating cells inflammatory arthritis synovium RAD21 5885 STMN1+ proliferating cells inflammatory arthritis synovium RAD23B 5887 STMN1+ proliferating cells inflammatory arthritis synovium RAD51 5888 STMN1+ proliferating cells inflammatory arthritis synovium RAD51AP1 10635 STMN1+ proliferating cells inflammatory arthritis synovium RAD54L 8438 STMN1+ proliferating cells inflammatory arthritis synovium RAN 5901 STMN1+ proliferating cells inflammatory arthritis synovium RANBP1 5902 STMN1+ proliferating cells inflammatory arthritis synovium RANGAP1 5905 STMN1+ proliferating cells inflammatory arthritis synovium RBBP4 5928 STMN1+ proliferating cells inflammatory arthritis synovium RBBP7 5931 STMN1+ proliferating cells inflammatory arthritis synovium RBM3 5935 STMN1+ proliferating cells inflammatory arthritis synovium RBM8A 9939 STMN1+ proliferating cells inflammatory arthritis synovium RCC1 1104 STMN1+ proliferating cells inflammatory arthritis synovium RCC2 55920 STMN1+ proliferating cells inflammatory arthritis synovium RDM1 201299 STMN1+ proliferating cells inflammatory arthritis synovium RDX 5962 STMN1+ proliferating cells inflammatory arthritis synovium RFC1 5981 STMN1+ proliferating cells inflammatory arthritis synovium RFC2 5982 STMN1+ proliferating cells inflammatory arthritis synovium RFC3 5983 STMN1+ proliferating cells inflammatory arthritis synovium RFC4 5984 STMN1+ proliferating cells inflammatory arthritis synovium RFC5 5985 STMN1+ proliferating cells inflammatory arthritis synovium RFWD3 55159 STMN1+ proliferating cells inflammatory arthritis synovium RHNO1 83695 STMN1+ proliferating cells inflammatory arthritis synovium RNASEH2A 10535 STMN1+ proliferating cells inflammatory arthritis synovium RNASEH2B 79621 STMN1+ proliferating cells inflammatory arthritis synovium RNASEH2C 84153 STMN1+ proliferating cells inflammatory arthritis synovium RNF19B 127544 STMN1+ proliferating cells inflammatory arthritis synovium RNF7 9616 STMN1+ proliferating cells inflammatory arthritis synovium RNPS1 10921 STMN1+ proliferating cells inflammatory arthritis synovium ROCK2 9475 STMN1+ proliferating cells inflammatory arthritis synovium RPA1 6117 STMN1+ proliferating cells inflammatory arthritis synovium RPA2 6118 STMN1+ proliferating cells inflammatory arthritis synovium RPA3 6119 STMN1+ proliferating cells inflammatory arthritis synovium RPL10A 4736 STMN1+ proliferating cells inflammatory arthritis synovium RPL12 6136 STMN1+ proliferating cells inflammatory arthritis synovium RPL13A 23521 STMN1+ proliferating cells inflammatory arthritis synovium RPL14 9045 STMN1+ proliferating cells inflammatory arthritis synovium RPL18 6141 STMN1+ proliferating cells inflammatory arthritis synovium RPL21 6144 STMN1+ proliferating cells inflammatory arthritis synovium RPL22 6146 STMN1+ proliferating cells inflammatory arthritis synovium RPL22L1 200916 STMN1+ proliferating cells inflammatory arthritis synovium RPL23 9349 STMN1+ proliferating cells inflammatory arthritis synovium RPL28 6158 STMN1+ proliferating cells inflammatory arthritis synovium RPL30 6156 STMN1+ proliferating cells inflammatory arthritis synovium RPL31 6160 STMN1+ proliferating cells inflammatory arthritis synovium RPL32 6161 STMN1+ proliferating cells inflammatory arthritis synovium RPL35 11224 STMN1+ proliferating cells inflammatory arthritis synovium RPL35A 6165 STMN1+ proliferating cells inflammatory arthritis synovium RPL36 25873 STMN1+ proliferating cells inflammatory arthritis synovium RPL36A 6173 STMN1+ proliferating cells inflammatory arthritis synovium RPL37A 6168 STMN1+ proliferating cells inflammatory arthritis synovium RPL38 6169 STMN1+ proliferating cells inflammatory arthritis synovium RPL39 6170 STMN1+ proliferating cells inflammatory arthritis synovium RPL5 6125 STMN1+ proliferating cells inflammatory arthritis synovium RPLP1 6176 STMN1+ proliferating cells inflammatory arthritis synovium RPLP2 6181 STMN1+ proliferating cells inflammatory arthritis synovium RPS10 6204 STMN1+ proliferating cells inflammatory arthritis synovium RPS12 6206 STMN1+ proliferating cells inflammatory arthritis synovium RPS13 6207 STMN1+ proliferating cells inflammatory arthritis synovium RPS15 6209 STMN1+ proliferating cells inflammatory arthritis synovium RPS15A 6210 STMN1+ proliferating cells inflammatory arthritis synovium RPS17 6218 STMN1+ proliferating cells inflammatory arthritis synovium RPS18 6222 STMN1+ proliferating cells inflammatory arthritis synovium RPS19 6223 STMN1+ proliferating cells inflammatory arthritis synovium RPS19BP1 91582 STMN1+ proliferating cells inflammatory arthritis synovium RPS2 6187 STMN1+ proliferating cells inflammatory arthritis synovium RPS20 6224 STMN1+ proliferating cells inflammatory arthritis synovium RPS21 6227 STMN1+ proliferating cells inflammatory arthritis synovium RPS24 6229 STMN1+ proliferating cells inflammatory arthritis synovium RPS26 6231 STMN1+ proliferating cells inflammatory arthritis synovium RPS27A 6233 STMN1+ proliferating cells inflammatory arthritis synovium RPS27L 51065 STMN1+ proliferating cells inflammatory arthritis synovium RPS3A 6189 STMN1+ proliferating cells inflammatory arthritis synovium RPS5 6193 STMN1+ proliferating cells inflammatory arthritis synovium RPS8 6202 STMN1+ proliferating cells inflammatory arthritis synovium RPSA 3921 STMN1+ proliferating cells inflammatory arthritis synovium RRM1 6240 STMN1+ proliferating cells inflammatory arthritis synovium RRM2 6241 STMN1+ proliferating cells inflammatory arthritis synovium RSL1D1 26156 STMN1+ proliferating cells inflammatory arthritis synovium S100A10 6281 STMN1+ proliferating cells inflammatory arthritis synovium S100A4 6275 STMN1+ proliferating cells inflammatory arthritis synovium SAE1 10055 STMN1+ proliferating cells inflammatory arthritis synovium SDC3 9672 STMN1+ proliferating cells inflammatory arthritis synovium SDHD 6392 STMN1+ proliferating cells inflammatory arthritis synovium SEC11C 90701 STMN1+ proliferating cells inflammatory arthritis synovium SEC31A 22872 STMN1+ proliferating cells inflammatory arthritis synovium SELENOH 280636 STMN1+ proliferating cells inflammatory arthritis synovium SERBP1 26135 STMN1+ proliferating cells inflammatory arthritis synovium SET 6418 STMN1+ proliferating cells inflammatory arthritis synovium SF3A3 10946 STMN1+ proliferating cells inflammatory arthritis synovium SF3B3 23450 STMN1+ proliferating cells inflammatory arthritis synovium SF3B5 83443 STMN1+ proliferating cells inflammatory arthritis synovium SFPQ 6421 STMN1+ proliferating cells inflammatory arthritis synovium SFXN1 94081 STMN1+ proliferating cells inflammatory arthritis synovium SGO1 151648 STMN1+ proliferating cells inflammatory arthritis synovium SGO2 151246 STMN1+ proliferating cells inflammatory arthritis synovium SHCBP1 79801 STMN1+ proliferating cells inflammatory arthritis synovium SHMT2 6472 STMN1+ proliferating cells inflammatory arthritis synovium SIVA1 10572 STMN1+ proliferating cells inflammatory arthritis synovium SKA1 220134 STMN1+ proliferating cells inflammatory arthritis synovium SLBP 7884 STMN1+ proliferating cells inflammatory arthritis synovium SLC1A5 6510 STMN1+ proliferating cells inflammatory arthritis synovium SLC25A10 1468 STMN1+ proliferating cells inflammatory arthritis synovium SLC25A4 291 STMN1+ proliferating cells inflammatory arthritis synovium SLC25A5 292 STMN1+ proliferating cells inflammatory arthritis synovium SLC29A1 2030 STMN1+ proliferating cells inflammatory arthritis synovium SLC4A7 9497 STMN1+ proliferating cells inflammatory arthritis synovium SLFN13 146857 STMN1+ proliferating cells inflammatory arthritis synovium SLIRP 81892 STMN1+ proliferating cells inflammatory arthritis synovium SMARCA5 8467 STMN1+ proliferating cells inflammatory arthritis synovium SMC1A 8243 STMN1+ proliferating cells inflammatory arthritis synovium SMC2 10592 STMN1+ proliferating cells inflammatory arthritis synovium SMC3 9126 STMN1+ proliferating cells inflammatory arthritis synovium SMC4 10051 STMN1+ proliferating cells inflammatory arthritis synovium SMC6 79677 STMN1+ proliferating cells inflammatory arthritis synovium SMCHD1 23347 STMN1+ proliferating cells inflammatory arthritis synovium SMS 6611 STMN1+ proliferating cells inflammatory arthritis synovium SMYD2 56950 STMN1+ proliferating cells inflammatory arthritis synovium SNHG6 641638 STMN1+ proliferating cells inflammatory arthritis synovium SNRNP25 79622 STMN1+ proliferating cells inflammatory arthritis synovium SNRNP27 11017 STMN1+ proliferating cells inflammatory arthritis synovium SNRNP70 6625 STMN1+ proliferating cells inflammatory arthritis synovium SNRPA1 6627 STMN1+ proliferating cells inflammatory arthritis synovium SNRPB 6628 STMN1+ proliferating cells inflammatory arthritis synovium SNRPC 6631 STMN1+ proliferating cells inflammatory arthritis synovium SNRPD1 6632 STMN1+ proliferating cells inflammatory arthritis synovium SNRPD2 6633 STMN1+ proliferating cells inflammatory arthritis synovium SNRPD3 6634 STMN1+ proliferating cells inflammatory arthritis synovium SNRPE 6635 STMN1+ proliferating cells inflammatory arthritis synovium SNRPF 6636 STMN1+ proliferating cells inflammatory arthritis synovium SNRPG 6637 STMN1+ proliferating cells inflammatory arthritis synovium SNU13 4809 STMN1+ proliferating cells inflammatory arthritis synovium SOD1 6647 STMN1+ proliferating cells inflammatory arthritis synovium SPC24 147841 STMN1+ proliferating cells inflammatory arthritis synovium SPC25 57405 STMN1+ proliferating cells inflammatory arthritis synovium SPCS3 60559 STMN1+ proliferating cells inflammatory arthritis synovium SPN 6693 STMN1+ proliferating cells inflammatory arthritis synovium SRM 6723 STMN1+ proliferating cells inflammatory arthritis synovium SRRM1 10250 STMN1+ proliferating cells inflammatory arthritis synovium SRSF1 6426 STMN1+ proliferating cells inflammatory arthritis synovium SRSF10 10772 STMN1+ proliferating cells inflammatory arthritis synovium SRSF2 6427 STMN1+ proliferating cells inflammatory arthritis synovium SRSF3 6428 STMN1+ proliferating cells inflammatory arthritis synovium SRSF7 6432 STMN1+ proliferating cells inflammatory arthritis synovium SSB 6741 STMN1+ proliferating cells inflammatory arthritis synovium SSNA1 8636 STMN1+ proliferating cells inflammatory arthritis synovium SSRP1 6749 STMN1+ proliferating cells inflammatory arthritis synovium STIP1 10963 STMN1+ proliferating cells inflammatory arthritis synovium STMN1 3925 STMN1+ proliferating cells inflammatory arthritis synovium STUB1 10273 STMN1+ proliferating cells inflammatory arthritis synovium SUPT16H 11198 STMN1+ proliferating cells inflammatory arthritis synovium SUZ12 23512 STMN1+ proliferating cells inflammatory arthritis synovium SYCE2 256126 STMN1+ proliferating cells inflammatory arthritis synovium SYNCRIP 10492 STMN1+ proliferating cells inflammatory arthritis synovium TACC3 10460 STMN1+ proliferating cells inflammatory arthritis synovium TAGLN2 8407 STMN1+ proliferating cells inflammatory arthritis synovium TARDBP 23435 STMN1+ proliferating cells inflammatory arthritis synovium TCEAL9 51186 STMN1+ proliferating cells inflammatory arthritis synovium TCF3 6929 STMN1+ proliferating cells inflammatory arthritis synovium TCP1 6950 STMN1+ proliferating cells inflammatory arthritis synovium TEX30 93081 STMN1+ proliferating cells inflammatory arthritis synovium TFDP1 7027 STMN1+ proliferating cells inflammatory arthritis synovium TFRC 7037 STMN1+ proliferating cells inflammatory arthritis synovium THOC7 80145 STMN1+ proliferating cells inflammatory arthritis synovium TIAL1 7073 STMN1+ proliferating cells inflammatory arthritis synovium TIMM13 26517 STMN1+ proliferating cells inflammatory arthritis synovium TIMM50 92609 STMN1+ proliferating cells inflammatory arthritis synovium TIMM8A 1678 STMN1+ proliferating cells inflammatory arthritis synovium TIPIN 54962 STMN1+ proliferating cells inflammatory arthritis synovium TK1 7083 STMN1+ proliferating cells inflammatory arthritis synovium TMEM107 84314 STMN1+ proliferating cells inflammatory arthritis synovium TMEM97 27346 STMN1+ proliferating cells inflammatory arthritis synovium TMPO 7112 STMN1+ proliferating cells inflammatory arthritis synovium TOMM20 9804 STMN1+ proliferating cells inflammatory arthritis synovium TOMM5 401505 STMN1+ proliferating cells inflammatory arthritis synovium TOMM7 54543 STMN1+ proliferating cells inflammatory arthritis synovium TOMM70A 9868 STMN1+ proliferating cells inflammatory arthritis synovium TOP2A 7153 STMN1+ proliferating cells inflammatory arthritis synovium TOPBP1 11073 STMN1+ proliferating cells inflammatory arthritis synovium TPM4 7171 STMN1+ proliferating cells inflammatory arthritis synovium TPX2 22974 STMN1+ proliferating cells inflammatory arthritis synovium TRIM28 10155 STMN1+ proliferating cells inflammatory arthritis synovium TRIM59 286827 STMN1+ proliferating cells inflammatory arthritis synovium TRIP13 9319 STMN1+ proliferating cells inflammatory arthritis synovium TSC22D1 8848 STMN1+ proliferating cells inflammatory arthritis synovium TSFM 10102 STMN1+ proliferating cells inflammatory arthritis synovium TSSC4 10078 STMN1+ proliferating cells inflammatory arthritis synovium TUBA1B 10376 STMN1+ proliferating cells inflammatory arthritis synovium TUBA1C 84790 STMN1+ proliferating cells inflammatory arthritis synovium TUBB 203068 STMN1+ proliferating cells inflammatory arthritis synovium TUBB2A 7280 STMN1+ proliferating cells inflammatory arthritis synovium TUBB4B 10383 STMN1+ proliferating cells inflammatory arthritis synovium TUBB6 84617 STMN1+ proliferating cells inflammatory arthritis synovium TUBG1 7283 STMN1+ proliferating cells inflammatory arthritis synovium TXN 7295 STMN1+ proliferating cells inflammatory arthritis synovium TXNL1 9352 STMN1+ proliferating cells inflammatory arthritis synovium TXNRD1 7296 STMN1+ proliferating cells inflammatory arthritis synovium TYMS 7298 STMN1+ proliferating cells inflammatory arthritis synovium U2AF1 7307 STMN1+ proliferating cells inflammatory arthritis synovium UBA2 10054 STMN1+ proliferating cells inflammatory arthritis synovium UBALD2 283991 STMN1+ proliferating cells inflammatory arthritis synovium UBE2C 11065 STMN1+ proliferating cells inflammatory arthritis synovium UBE2S 27338 STMN1+ proliferating cells inflammatory arthritis synovium UBE2T 29089 STMN1+ proliferating cells inflammatory arthritis synovium UCHL5 51377 STMN1+ proliferating cells inflammatory arthritis synovium UHRF1 29128 STMN1+ proliferating cells inflammatory arthritis synovium UQCC2 84300 STMN1+ proliferating cells inflammatory arthritis synovium UQCR10 29796 STMN1+ proliferating cells inflammatory arthritis synovium UQCR11 10975 STMN1+ proliferating cells inflammatory arthritis synovium UQCRFS1 7386 STMN1+ proliferating cells inflammatory arthritis synovium UQCRQ 27089 STMN1+ proliferating cells inflammatory arthritis synovium USMG5 84833 STMN1+ proliferating cells inflammatory arthritis synovium USP1 7398 STMN1+ proliferating cells inflammatory arthritis synovium VARS 7407 STMN1+ proliferating cells inflammatory arthritis synovium VCP 7415 STMN1+ proliferating cells inflammatory arthritis synovium VDAC1 7416 STMN1+ proliferating cells inflammatory arthritis synovium VDAC2 7417 STMN1+ proliferating cells inflammatory arthritis synovium VIM 7431 STMN1+ proliferating cells inflammatory arthritis synovium VMA21 203547 STMN1+ proliferating cells inflammatory arthritis synovium VRK1 7443 STMN1+ proliferating cells inflammatory arthritis synovium WAPL 23063 STMN1+ proliferating cells inflammatory arthritis synovium WDR43 23160 STMN1+ proliferating cells inflammatory arthritis synovium WDR89 112840 STMN1+ proliferating cells inflammatory arthritis synovium XPO1 7514 STMN1+ proliferating cells inflammatory arthritis synovium YBX1 4904 STMN1+ proliferating cells inflammatory arthritis synovium YBX3 8531 STMN1+ proliferating cells inflammatory arthritis synovium YWHAH 7533 STMN1+ proliferating cells inflammatory arthritis synovium ZC3H15 55854 STMN1+ proliferating cells inflammatory arthritis synovium ADAM28 10863 HBEGF+ proinflammatory macrophages ADAMDEC1 27299 HBEGF+ proinflammatory macrophages ANKRD37 353322 HBEGF+ proinflammatory macrophages ARL4A 10124 HBEGF+ proinflammatory macrophages ARL5B 221079 HBEGF+ proinflammatory macrophages ATF3 467 HBEGF+ proinflammatory macrophages B4GALT1 2683 HBEGF+ proinflammatory macrophages BIRC3 330 HBEGF+ proinflammatory macrophages CCNH 902 HBEGF+ proinflammatory macrophages CHML 1122 HBEGF+ proinflammatory macrophages CHMP1B 57132 HBEGF+ proinflammatory macrophages CREM 1390 HBEGF+ proinflammatory macrophages CSRNP1 64651 HBEGF+ proinflammatory macrophages CXCL2 2920 HBEGF+ proinflammatory macrophages CXCL3 2921 HBEGF+ proinflammatory macrophages CXCL8 3576 HBEGF+ proinflammatory macrophages CYB5D1 124637 HBEGF+ proinflammatory macrophages DDX3Y 8653 HBEGF+ proinflammatory macrophages DNAJA4 55466 HBEGF+ proinflammatory macrophages DNAJB1 3337 HBEGF+ proinflammatory macrophages DNAJB6 10049 HBEGF+ proinflammatory macrophages DUSP2 1844 HBEGF+ proinflammatory macrophages EGR1 1958 HBEGF+ proinflammatory macrophages EGR3 1960 HBEGF+ proinflammatory macrophages EREG 2069 HBEGF+ proinflammatory macrophages ERN1 2081 HBEGF+ proinflammatory macrophages FCER1A 2205 HBEGF+ proinflammatory macrophages FOSB 2354 HBEGF+ proinflammatory macrophages FOSL2 2355 HBEGF+ proinflammatory macrophages GLA 2717 HBEGF+ proinflammatory macrophages GPR183 1880 HBEGF+ proinflammatory macrophages GRASP 160622 HBEGF+ proinflammatory macrophages HBEGF 1839 HBEGF+ proinflammatory macrophages HNRNPU-AS1 284702 HBEGF+ proinflammatory macrophages HSP90AA1 3320 HBEGF+ proinflammatory macrophages HSPA1A 3303 HBEGF+ proinflammatory macrophages HSPA1B 3304 HBEGF+ proinflammatory macrophages HSPD1 3329 HBEGF+ proinflammatory macrophages HSPH1 10808 HBEGF+ proinflammatory macrophages IER2 9592 HBEGF+ proinflammatory macrophages IER3 8870 HBEGF+ proinflammatory macrophages IL1B 3553 HBEGF+ proinflammatory macrophages INSIG1 3638 HBEGF+ proinflammatory macrophages JMY 133746 HBEGF+ proinflammatory macrophages JUNB 3726 HBEGF+ proinflammatory macrophages KDM6B 23135 HBEGF+ proinflammatory macrophages LDLR 3949 HBEGF+ proinflammatory macrophages MAFF 23764 HBEGF+ proinflammatory macrophages MIR24-2 407013 HBEGF+ proinflammatory macrophages MIR29B1 407024 HBEGF+ proinflammatory macrophages MXD1 4084 HBEGF+ proinflammatory macrophages NFIL3 4783 HBEGF+ proinflammatory macrophages NFKBID 84807 HBEGF+ proinflammatory macrophages NR4A1 3164 HBEGF+ proinflammatory macrophages NR4A2 4929 HBEGF+ proinflammatory macrophages NR4A3 8013 HBEGF+ proinflammatory macrophages NRARP 441478 HBEGF+ proinflammatory macrophages PFKFB3 5209 HBEGF+ proinflammatory macrophages PHACTR1 221692 HBEGF+ proinflammatory macrophages PLAUR 5329 HBEGF+ proinflammatory macrophages PRMT9 90826 HBEGF+ proinflammatory macrophages PTGER4 5734 HBEGF+ proinflammatory macrophages PTGS2 5743 HBEGF+ proinflammatory macrophages RASSF5 83593 HBEGF+ proinflammatory macrophages RGS2 5997 HBEGF+ proinflammatory macrophages RHOB 388 HBEGF+ proinflammatory macrophages RN7SL368P 1.06E+08 HBEGF+ proinflammatory macrophages SATB1 6304 HBEGF+ proinflammatory macrophages SELK 58515 HBEGF+ proinflammatory macrophages SEMA4A 64218 HBEGF+ proinflammatory macrophages SIK1 150094 HBEGF+ proinflammatory macrophages SLC25A44 9673 HBEGF+ proinflammatory macrophages SOCS3 9021 HBEGF+ proinflammatory macrophages SYAP1 94056 HBEGF+ proinflammatory macrophages THBS1 7057 HBEGF+ proinflammatory macrophages TNFAIP3 7128 HBEGF+ proinflammatory macrophages TSPYL2 64061 HBEGF+ proinflammatory macrophages USP36 57602 HBEGF+ proinflammatory macrophages VEGFA 7422 HBEGF+ proinflammatory macrophages ZFP36 7538 HBEGF+ proinflammatory macrophages ZNF331 55422 HBEGF+ proinflammatory macrophages ALDOA 226 IFN-activated macrophages APOBEC3A 200315 IFN-activated macrophages AQP9 366 IFN-activated macrophages C15orf48 84419 IFN-activated macrophages CD300E 342510 IFN-activated macrophages CD36 948 IFN-activated macrophages CD52 1043 IFN-activated macrophages CSTB 1476 IFN-activated macrophages ENO1 2023 IFN-activated macrophages ENO2 2026 IFN-activated macrophages FAM65B 9750 IFN-activated macrophages FCN1 2219 IFN-activated macrophages FN1 2335 IFN-activated macrophages GAPDH 2597 IFN-activated macrophages IFI44L 10964 IFN-activated macrophages IFI6 2537 IFN-activated macrophages IGHM 3507 IFN-activated macrophages ISG15 9636 IFN-activated macrophages ITGB7 3695 IFN-activated macrophages LPL 4023 IFN-activated macrophages LY6E 4061 IFN-activated macrophages MT1E 4493 IFN-activated macrophages MT1F 4494 IFN-activated macrophages MT1G 4495 IFN-activated macrophages MT1X 4501 IFN-activated macrophages MT2A 4502 IFN-activated macrophages OPTN 10133 IFN-activated macrophages S100A8 6279 IFN-activated macrophages SLAMF7 57823 IFN-activated macrophages SPP1 6696 IFN-activated macrophages TGM2 7052 IFN-activated macrophages TIMP1 7076 IFN-activated macrophages VCAN 1462 IFN-activated macrophages WARS 7453 IFN-activated macrophages ABCB10 23456 Phagocytic macrophages ABCC3 8714 Phagocytic macrophages ACAD9 28976 Phagocytic macrophages ACSM5 54988 Phagocytic macrophages ACTL6A 86 Phagocytic macrophages ADAM12 8038 Phagocytic macrophages ADORA3 140 Phagocytic macrophages ADRB2 154 Phagocytic macrophages AHNAK2 113146 Phagocytic macrophages AIFM2 84883 Phagocytic macrophages ALS2 57679 Phagocytic macrophages ANKH 56172 Phagocytic macrophages AP3M1 26985 Phagocytic macrophages ARMC9 80210 Phagocytic macrophages ARSB 411 Phagocytic macrophages ASAP2 8853 Phagocytic macrophages ASB1 51665 Phagocytic macrophages B3GNT7 93010 Phagocytic macrophages BLOC1S5 63915 Phagocytic macrophages BRIX1 55299 Phagocytic macrophages BTD 686 Phagocytic macrophages C11orf68 83638 Phagocytic macrophages CALU 813 Phagocytic macrophages CCT5 22948 Phagocytic macrophages CD109 135228 Phagocytic macrophages CD276 80381 Phagocytic macrophages CD28 940 Phagocytic macrophages CD3EAP 10849 Phagocytic macrophages CD9 928 Phagocytic macrophages CDR2 1039 Phagocytic macrophages CHST13 166012 Phagocytic macrophages CRIP2 1397 Phagocytic macrophages CRYBB1 1414 Phagocytic macrophages CSPG4 1464 Phagocytic macrophages CSTF2T 23283 Phagocytic macrophages CTSK 1513 Phagocytic macrophages CXADR 1525 Phagocytic macrophages DAAM1 23002 Phagocytic macrophages DCBLD2 131566 Phagocytic macrophages DIP2C 22982 Phagocytic macrophages DLEU7 220107 Phagocytic macrophages DNM1 1759 Phagocytic macrophages EFNB1 1947 Phagocytic macrophages EMC1 23065 Phagocytic macrophages EMP1 2012 Phagocytic macrophages EPN2 22905 Phagocytic macrophages ERMARD 55780 Phagocytic macrophages EXOG 9941 Phagocytic macrophages EXOSC8 11340 Phagocytic macrophages EXTL2 2135 Phagocytic macrophages EYA2 2139 Phagocytic macrophages FAIM 55179 Phagocytic macrophages FAM134B 54463 Phagocytic macrophages FASTKD5 60493 Phagocytic macrophages FBLN5 10516 Phagocytic macrophages FBXO32 114907 Phagocytic macrophages FERMT2 10979 Phagocytic macrophages FGD5 152273 Phagocytic macrophages FUCA1 2517 Phagocytic macrophages FYCO1 79443 Phagocytic macrophages GABRB2 2561 Phagocytic macrophages GATB 5188 Phagocytic macrophages GCHFR 2644 Phagocytic macrophages GLDN 342035 Phagocytic macrophages GNG12 55970 Phagocytic macrophages GNPNAT1 64841 Phagocytic macrophages GOT1 2805 Phagocytic macrophages GPNMB 10457 Phagocytic macrophages GPR34 2857 Phagocytic macrophages GSDMA 284110 Phagocytic macrophages GSTT1 2952 Phagocytic macrophages HDHD1 8226 Phagocytic macrophages HOXB6 3216 Phagocytic macrophages HPGDS 27306 Phagocytic macrophages HTRA1 5654 Phagocytic macrophages IGSF21 84966 Phagocytic macrophages ITGA6 3655 Phagocytic macrophages ITGAE 3682 Phagocytic macrophages ITGB5 3693 Phagocytic macrophages KAL1 3730 Phagocytic macrophages KANK1 23189 Phagocytic macrophages KANK2 25959 Phagocytic macrophages KCNQ3 3786 Phagocytic macrophages KCTD10 83892 Phagocytic macrophages KLF9 687 Phagocytic macrophages L1TD1 54596 Phagocytic macrophages LAMC1 3915 Phagocytic macrophages LGI2 55203 Phagocytic macrophages LGMN 5641 Phagocytic macrophages LILRB5 10990 Phagocytic macrophages LRRC8A 56262 Phagocytic macrophages LZTR1 8216 Phagocytic macrophages MCOLN3 55283 Phagocytic macrophages MERTK 10461 Phagocytic macrophages MLF1 4291 Phagocytic macrophages MMD 23531 Phagocytic macrophages MMP2 4313 Phagocytic macrophages MRPS14 63931 Phagocytic macrophages MRS2 57380 Phagocytic macrophages MSMO1 6307 Phagocytic macrophages MTUS1 57509 Phagocytic macrophages NAA30 122830 Phagocytic macrophages NAT9 26151 Phagocytic macrophages NFU1 27247 Phagocytic macrophages NRBP2 340371 Phagocytic macrophages NUDCD2 134492 Phagocytic macrophages OAT 4942 Phagocytic macrophages OLFML3 56944 Phagocytic macrophages PAQR5 54852 Phagocytic macrophages PAX8 7849 Phagocytic macrophages PDCD11 22984 Phagocytic macrophages PDE1B 5153 Phagocytic macrophages PDK4 5166 Phagocytic macrophages PDPN 10630 Phagocytic macrophages PGM2 55276 Phagocytic macrophages PGM5 5239 Phagocytic macrophages PIK3CG 5294 Phagocytic macrophages PLEK2 26499 Phagocytic macrophages PMP22 5376 Phagocytic macrophages POLM 27434 Phagocytic macrophages PPIP5K1 9677 Phagocytic macrophages PPM1N 147699 Phagocytic macrophages PRKCDBP 112464 Phagocytic macrophages PROS1 5627 Phagocytic macrophages PTGFRN 5738 Phagocytic macrophages PTPRM 5797 Phagocytic macrophages PTPRN2 5799 Phagocytic macrophages PYCARD-AS1 1.01E+08 Phagocytic macrophages RAB11FIP5 26056 Phagocytic macrophages RAE1 8480 Phagocytic macrophages RBP4 5950 Phagocytic macrophages RGL3 57139 Phagocytic macrophages RIOK1 83732 Phagocytic macrophages RMDN3 55177 Phagocytic macrophages RND3 390 Phagocytic macrophages RPS6KA2 6196 Phagocytic macrophages RRAGA 10670 Phagocytic macrophages S1PR1 1901 Phagocytic macrophages SEMA4B 10509 Phagocytic macrophages SEPTIN10 151011 Phagocytic macrophages SLC16A6 9120 Phagocytic macrophages SLC1A3 6507 Phagocytic macrophages SLC25A43 203427 Phagocytic macrophages SLC26A11 284129 Phagocytic macrophages SLC29A1 2030 Phagocytic macrophages SLC43A3 29015 Phagocytic macrophages SLC6A12 6539 Phagocytic macrophages SNCA 6622 Phagocytic macrophages ST5 6764 Phagocytic macrophages STEAP3 55240 Phagocytic macrophages SYT1 6857 Phagocytic macrophages TBC1D2 55357 Phagocytic macrophages TBCE 6905 Phagocytic macrophages TDP2 51567 Phagocytic macrophages TDRD10 126668 Phagocytic macrophages TGFBR1 7046 Phagocytic macrophages THRB 7068 Phagocytic macrophages TIMM10 26519 Phagocytic macrophages TMEM106C 79022 Phagocytic macrophages TMEM119 338773 Phagocytic macrophages TMEM255B 348013 Phagocytic macrophages TNFAIP8L3 388121 Phagocytic macrophages TNFRSF10D 8793 Phagocytic macrophages TNFRSF11A 8792 Phagocytic macrophages TNS1 7145 Phagocytic macrophages TPPP3 51673 Phagocytic macrophages TREML1 340205 Phagocytic macrophages TRIM21 6737 Phagocytic macrophages TRIM47 91107 Phagocytic macrophages TRIM58 25893 Phagocytic macrophages TUBB2A 7280 Phagocytic macrophages TUBB6 84617 Phagocytic macrophages TUBG1 7283 Phagocytic macrophages TXNRD2 10587 Phagocytic macrophages UEVLD 55293 Phagocytic macrophages UNC5B 219699 Phagocytic macrophages VANGL1 81839 Phagocytic macrophages VPS33A 65082 Phagocytic macrophages WDR12 55759 Phagocytic macrophages WDR77 79084 Phagocytic macrophages ZBED3-AS1 728723 Phagocytic macrophages ZBTB7C 201501 Phagocytic macrophages ZNF83 55769 Phagocytic macrophages AK3 50808 M1 APOL1 8542 M1 APOL2 23780 M1 APOL3 80833 M1 APOL6 80830 M1 ATF3 467 M1 BCL2A1 597 M1 BIRC3 330 M1 CCL15 6359 M1 CCL19 6363 M1 CCL20 6364 M1 CCL5 6352 M1 CCR7 1236 M1 CHI3L2 1117 M1 CXCL10 3627 M1 CXCL11 6373 M1 CXCL9 4283 M1 EDN1 1906 M1 FAS 355 M1 GADD45G 10912 M1 HESX1 8820 M1 HSD11B1 3290 M1 IDO1 3620 M1 IGFBP4 3487 M1 IL12B 3593 M1 IL15 3600 M1 IL15RA 3601 M1 IL2RA 3559 M1 IL6 3569 M1 IL7R 3575 M1 INHBA 3624 M1 IRF1 3659 M1 IRF7 3665 M1 NAMPT 10135 M1 OAS2 4939 M1 OASL 8638 M1 PDGFA 5154 M1 PFKFB3 5209 M1 PFKP 5214 M1 PLA1A 51365 M1 PSMA2 5683 M1 PSMB9 5698 M1 PSME2 5721 M1 PTX3 5806 M1 SCO2 9997 M1 SLC2A6 11182 M1 SLC31A2 1318 M1 SLC7A5 8140 M1 SLCO5A1 81796 M1 SPHK1 8877 M1 TNF 7124 M1 TNFSF10 8743 M1 VCAN 1462 M1 XAF1 54739 M1 ADK 132 M2 ALOX15 246 M2 CA2 760 M2 CCL13 6357 M2 CCL18 6362 M2 CCL23 6368 M2 CD209 30835 M2 CD36 948 M2 CERK 64781 M2 CHN2 1124 M2 CLEC4F 165530 M2 CLEC7A 64581 M2 CTSC 1075 M2 CXCR4 7852 M2 DLC1 10395 M2 EGR2 1959 M2 FGL2 10875 M2 FN1 2335 M2 GAS7 8522 M2 HEXB 3074 M2 HNMT 3176 M2 HRH1 3269 M2 HS3ST1 9957 M2 HS3ST2 9956 M2 IGF1 3479 M2 LIPA 3988 M2 LPAR6 10161 M2 LTA4H 4048 M2 MAF 4094 M2 MRC1 4360 M2 MS4A4A 51338 M2 MS4A6A 64231 M2 MSR1 4481 M2 P2RY13 53829 M2 P2RY14 9934 M2 SELENOP 6414 M2 SLC38A6 145389 M2 SLC4A7 9497 M2 SLCO2B1 11309 M2 TGFBI 7045 M2 TGFBR2 7048 M2 TLR5 7100 M2 TPST2 8459 M2 ARAP2 116984 Martinez S4 ARID5B 84159 Martinez S4 ARNTL2 56938 Martinez S4 BATF3 55509 Martinez S4 CCL14 6358 Martinez S4 CCL8 6355 Martinez S4 CD274 29126 Martinez S4 CD38 952 Martinez S4 CFB 629 Martinez S4 CKB 1152 Martinez S4 CXCL13 10563 Martinez S4 EBI3 10148 Martinez S4 FBX06 26270 Martinez S4 GADD45A 1647 Martinez S4 GADD45B 4616 Martinez S4 GLS 2744 Martinez S4 GOLM1 51280 Martinez S4 GTDC1 79712 Martinez S4 IFI27 3429 Martinez S4 IFITM1 8519 Martinez S4 IL21R 50615 Martinez S4 IL32 9235 Martinez S4 JAK3 3718 Martinez S4 KCNJ2 3759 Martinez S4 LHFPL6 10186 Martinez S4 LY75 4065 Martinez S4 MMP12 4321 Martinez S4 MMP25 64386 Martinez S4 MT1M 4499 Martinez S4 N4BP1 9683 Martinez S4 NBN 4683 Martinez S4 PDCD1LG2 80380 Martinez S4 PXYLP1 92370 Martinez S4 RASGRP1 10125 Martinez S4 SERPINB9 5272 Martinez S4 SERPING1 710 Martinez S4 SLAMF1 6504 Martinez S4 SOCS1 8651 Martinez S4 ST7 7982 Martinez S4 TIFA 92610 Martinez S4 TSPAN33 340348 Martinez S4 VCAM1 7412 Martinez S4 ADAMTS14 140766 Martinez S5 CISH 1154 Martinez S5 GGT5 2687 Martinez S5 MAG11 9223 Martinez S5 MAOA 4128 Martinez S5 STAMBPL1 57559 Martinez S5 SULF2 55959 Martinez S5 TTC9C 283237 Martinez S5 CCL11 6356 RnD M1 CCL15 6359 RnD M1 CCL19 6363 RnD M1 CCL2 6347 RnD M1 CCL20 6364 RnD M1 CCL3 6348 RnD M1 CCL4 6351 RnD M1 CCL5 6352 RnD M1 CCL8 6355 RnD M1 CD163 9332 RnD M1 CD36 948 RnD M1 CD68 968 RnD M1 CD80 941 RnD M1 CD86 942 RnD M1 COX2 4513 RnD M1 CX3CL1 6376 RnD M1 CXCL1 2919 RnD M1 CXCL10 3627 RnD M1 CXCL11 6373 RnD M1 CXCL13 10563 RnD M1 CXCL16 58191 RnD M1 CXCL2 2920 RnD M1 CXCL3 2921 RnD M1 CXCL5 6374 RnD M1 CXCL9 4283 RnD M1 FCGR2A 2212 RnD M1 FCGR3A 2214 RnD M1 HLA-DRA 3122 RnD M1 HLA-DRB1 3123 RnD M1 IFNG 3458 RnD M1 IFNGR1 3459 RnD M1 IL12A 3592 RnD M1 IL12B 3593 RnD M1 IL15 3600 RnD M1 IL17A 3605 RnD M1 IL18 3606 RnD M1 IL1B 3553 RnD M1 IL23A 51561 RnD M1 IL6 3569 RnD M1 IL8 3576 RnD M1 IRF5 3663 RnD M1 NOS2 4843 RnD M1 STAT1 6772 RnD M1 TNF 7124 RnD M1 ARG1 383 RnD M2a CCL1 6346 RnD M2a CCL14 6358 RnD M2a CCL17 6361 RnD M2a CCL18 6362 RnD M2a CCL2 6347 RnD M2a CCL22 6367 RnD M2a CCL23 6368 RnD M2a CCL24 6369 RnD M2a CCL26 10344 RnD M2a CD163 9332 RnD M2a CD200R1 131450 RnD M2a CD200R1L 344807 RnD M2a CD209 30835 RnD M2a CHI3L1 1116 RnD M2a CLEC10A 10462 RnD M2a CLEC7A 64581 RnD M2a CXCR1 3577 RnD M2a CXCR2 3579 RnD M2a FCER1A 2205 RnD M2a HLA-DRA 3122 RnD M2a HLA-DRB1 3123 RnD M2a IL10 3586 RnD M2a IL12A 3592 RnD M2a IL12B 3593 RnD M2a IL1R2 7850 RnD M2a IL1RN 3557 RnD M2a IRF4 3662 RnD M2a MRC1 4360 RnD M2a PPARG 5468 RnD M2a RETNLB 84666 RnD M2a STAT6 6778 RnD M2a TGFB1 7040 RnD M2a CD86 942 RnD M2b CCL1 6346 RnD M2b CCL20 6364 RnD M2b COX2 4513 RnD M2b CXCL1 2919 RnD M2b CXCL2 2920 RnD M2b CXCL3 2921 RnD M2b CSF3 1440 RnD M2b CSF2 1437 RnD M2b IL1B 3553 RnD M2b IL4R 3566 RnD M2b IL6 3569 RnD M2b IL10 3586 RnD M2b IRF4 3662 RnD M2b HLA-DRA 3122 RnD M2b HLA-DRB1 3123 RnD M2b SOCS3 9021 RnD M2b SPHK1 8877 RnD M2b SPHK2 56848 RnD M2b TNF 7124 RnD M2b ARG1 383 RnD M2c CCL16 6360 RnD M2c CCL18 6362 RnD M2c CCR2 729230 RnD M2c CD163 9332 RnD M2c CXCL13 10563 RnD M2c IL10 3586 RnD M2c IL4R 3566 RnD M2c INHBA 3624 RnD M2c IRF4 3662 RnD M2c MRC1 4360 RnD M2c MSR1 4481 RnD M2c SCARB1 949 RnD M2c SLAMF1 6504 RnD M2c SOCS3 9021 RnD M2c TGFB1 7040 RnD M2c TLR1 7096 RnD M2c TLR8 51311 RnD M2c CCL5 6352 RnD M2d CXCL10 3627 RnD M2d CXCL16 58191 RnD M2d IL10 3586 RnD M2d IL12A 3592 RnD M2d IL12B 3593 RnD M2d NOS2 4843 RnD M2d TNF 7124 RnD M2d VEGF 7422 RnD M2d APOE 348 Reyman alveolar macrophage top 12 CCL2 6347 Reyman alveolar macrophage top 12 CD36 948 Reyman alveolar macrophage top 12 CHI3L1 1116 Reyman alveolar macrophage top 12 FN1 2335 Reyman alveolar macrophage top 12 IL1RN 3557 Reyman alveolar macrophage top 12 MARCKS 4082 Reyman alveolar macrophage top 12 PLA2G7 7941 Reyman alveolar macrophage top 12 S100A8 6279 Reyman alveolar macrophage top 12 SPP1 6696 Reyman alveolar macrophage top 12 TIMP1 7076 Reyman alveolar macrophage top 12 TREM2 54209 Reyman alveolar macrophage top 12 A2M 2 Reyman alveolar macrophage complete UP ABCA1 19 Reyman alveolar macrophage complete UP ABHD2 11057 Reyman alveolar macrophage complete UP ACP2 53 Reyman alveolar macrophage complete UP ACTB 60 Reyman alveolar macrophage complete UP ACTG1 71 Reyman alveolar macrophage complete UP ADGRE5 976 Reyman alveolar macrophage complete UP ANXA2 302 Reyman alveolar macrophage complete UP APOC1 341 Reyman alveolar macrophage complete UP APOE 348 Reyman alveolar macrophage complete UP ARHGDIB 397 Reyman alveolar macrophage complete UP ARID5B 84159 Reyman alveolar macrophage complete UP ARPC1B 10095 Reyman alveolar macrophage complete UP ATOX1 475 Reyman alveolar macrophage complete UP ATP13A3 79572 Reyman alveolar macrophage complete UP ATP6V1B2 526 Reyman alveolar macrophage complete UP BASP1 10409 Reyman alveolar macrophage complete UP BCAT1 586 Reyman alveolar macrophage complete UP C15orf48 84419 Reyman alveolar macrophage complete UP C6orf62 81688 Reyman alveolar macrophage complete UP CALM3 808 Reyman alveolar macrophage complete UP CALR 811 Reyman alveolar macrophage complete UP CAP1 10487 Reyman alveolar macrophage complete UP CCL18 6362 Reyman alveolar macrophage complete UP CCL2 6347 Reyman alveolar macrophage complete UP CCL4 6351 Reyman alveolar macrophage complete UP CD14 929 Reyman alveolar macrophage complete UP CD36 948 Reyman alveolar macrophage complete UP CD4 920 Reyman alveolar macrophage complete UP CD44 960 Reyman alveolar macrophage complete UP CD48 962 Reyman alveolar macrophage complete UP CD84 8832 Reyman alveolar macrophage complete UP CD9 928 Reyman alveolar macrophage complete UP CDC42 998 Reyman alveolar macrophage complete UP CFL1 1072 Reyman alveolar macrophage complete UP CHI3L1 1116 Reyman alveolar macrophage complete UP CHIT1 1118 Reyman alveolar macrophage complete UP CLTC 1213 Reyman alveolar macrophage complete UP CMTM3 123920 Reyman alveolar macrophage complete UP CMTM6 54918 Reyman alveolar macrophage complete UP COTL1 23406 Reyman alveolar macrophage complete UP CPM 1368 Reyman alveolar macrophage complete UP CRIP1 1396 Reyman alveolar macrophage complete UP CSF1R 1436 Reyman alveolar macrophage complete UP CTSB 1508 Reyman alveolar macrophage complete UP CTSL 1514 Reyman alveolar macrophage complete UP CTSZ 1522 Reyman alveolar macrophage complete UP CYBB 1536 Reyman alveolar macrophage complete UP CYFIP1 23191 Reyman alveolar macrophage complete UP DPYSL2 1808 Reyman alveolar macrophage complete UP EMP1 2012 Reyman alveolar macrophage complete UP EVL 51466 Reyman alveolar macrophage complete UP FCGR2A 2212 Reyman alveolar macrophage complete UP FCGR2B 2213 Reyman alveolar macrophage complete UP FCGR3A 2214 Reyman alveolar macrophage complete UP FGL2 10875 Reyman alveolar macrophage complete UP FKBP1A 2280 Reyman alveolar macrophage complete UP FLNA 2316 Reyman alveolar macrophage complete UP FN1 2335 Reyman alveolar macrophage complete UP FPR3 2359 Reyman alveolar macrophage complete UP FUCA1 2517 Reyman alveolar macrophage complete UP FXYD5 53827 Reyman alveolar macrophage complete UP FYB 2533 Reyman alveolar macrophage complete UP GBP1 2633 Reyman alveolar macrophage complete UP GLIPR1 11010 Reyman alveolar macrophage complete UP GM2A 2760 Reyman alveolar macrophage complete UP GSN 2934 Reyman alveolar macrophage complete UP HCK 3055 Reyman alveolar macrophage complete UP HCST 10870 Reyman alveolar macrophage complete UP HIF1A 3091 Reyman alveolar macrophage complete UP HLA-A 3105 Reyman alveolar macrophage complete UP HLA-DQA2 3118 Reyman alveolar macrophage complete UP HMGN1 3150 Reyman alveolar macrophage complete UP IGF2R 3482 Reyman alveolar macrophage complete UP IGHG1 3500 Reyman alveolar macrophage complete UP IGHG3 3502 Reyman alveolar macrophage complete UP IGHG4 3503 Reyman alveolar macrophage complete UP IGKC 3514 Reyman alveolar macrophage complete UP IGLC2 3538 Reyman alveolar macrophage complete UP IGSF6 10261 Reyman alveolar macrophage complete UP IL1RN 3557 Reyman alveolar macrophage complete UP IL7R 3575 Reyman alveolar macrophage complete UP ITGAM 3684 Reyman alveolar macrophage complete UP ITGAX 3687 Reyman alveolar macrophage complete UP ITGB1 3688 Reyman alveolar macrophage complete UP ITGB2 3689 Reyman alveolar macrophage complete UP KIAA0930 23313 Reyman alveolar macrophage complete UP LAP3 51056 Reyman alveolar macrophage complete UP LASP1 3927 Reyman alveolar macrophage complete UP LCP1 3936 Reyman alveolar macrophage complete UP LDHA 3939 Reyman alveolar macrophage complete UP LGMN 5641 Reyman alveolar macrophage complete UP LHFPL2 10184 Reyman alveolar macrophage complete UP LILRB4 11006 Reyman alveolar macrophage complete UP LIPA 3988 Reyman alveolar macrophage complete UP LITAF 9516 Reyman alveolar macrophage complete UP LSP1 4046 Reyman alveolar macrophage complete UP LST1 7940 Reyman alveolar macrophage complete UP MAFB 9935 Reyman alveolar macrophage complete UP MARCKS 4082 Reyman alveolar macrophage complete UP MNDA 4332 Reyman alveolar macrophage complete UP MS4A4A 51338 Reyman alveolar macrophage complete UP MS4A6A 64231 Reyman alveolar macrophage complete UP MT-ATP6 4508 Reyman alveolar macrophage complete UP MT-ATP8 4509 Reyman alveolar macrophage complete UP MT-CO3 4514 Reyman alveolar macrophage complete UP MT-ND3 4537 Reyman alveolar macrophage complete UP MT-ND6 4541 Reyman alveolar macrophage complete UP NPC2 10577 Reyman alveolar macrophage complete UP NR1H3 10062 Reyman alveolar macrophage complete UP NRP2 8828 Reyman alveolar macrophage complete UP OLR1 4973 Reyman alveolar macrophage complete UP P4HB 5034 Reyman alveolar macrophage complete UP PDIA4 9601 Reyman alveolar macrophage complete UP PEA15 8682 Reyman alveolar macrophage complete UP PGK1 5230 Reyman alveolar macrophage complete UP PLA2G7 7941 Reyman alveolar macrophage complete UP PLAC8 51316 Reyman alveolar macrophage complete UP PLEK 5341 Reyman alveolar macrophage complete UP PPT1 5538 Reyman alveolar macrophage complete UP PSAP 5660 Reyman alveolar macrophage complete UP QSOX1 5768 Reyman alveolar macrophage complete UP RAB31 11031 Reyman alveolar macrophage complete UP RALA 5898 Reyman alveolar macrophage complete UP RGS1 5996 Reyman alveolar macrophage complete UP RNASE1 6035 Reyman alveolar macrophage complete UP S100A8 6279 Reyman alveolar macrophage complete UP S100A9 6280 Reyman alveolar macrophage complete UP SAMHD1 25939 Reyman alveolar macrophage complete UP SCGB3A1 92304 Reyman alveolar macrophage complete UP SDC2 6383 Reyman alveolar macrophage complete UP SDS 10993 Reyman alveolar macrophage complete UP SEPP1 6414 Reyman alveolar macrophage complete UP SGK1 6446 Reyman alveolar macrophage complete UP SH3BGRL3 83442 Reyman alveolar macrophage complete UP SLA 6503 Reyman alveolar macrophage complete UP SLC16A10 117247 Reyman alveolar macrophage complete UP SLC1A3 6507 Reyman alveolar macrophage complete UP SMIM3 85027 Reyman alveolar macrophage complete UP SOD2 6648 Reyman alveolar macrophage complete UP SPARC 6678 Reyman alveolar macrophage complete UP SPP1 6696 Reyman alveolar macrophage complete UP SRGN 5552 Reyman alveolar macrophage complete UP SRSF2 6427 Reyman alveolar macrophage complete UP STAT1 6772 Reyman alveolar macrophage complete UP TGFBI 7045 Reyman alveolar macrophage complete UP TGM2 7052 Reyman alveolar macrophage complete UP TIMP1 7076 Reyman alveolar macrophage complete UP TLN1 7094 Reyman alveolar macrophage complete UP TMEM176B 28959 Reyman alveolar macrophage complete UP TMSB10 9168 Reyman alveolar macrophage complete UP TMSB4X 7114 Reyman alveolar macrophage complete UP TNFSF13B 10673 Reyman alveolar macrophage complete UP TPM3 7170 Reyman alveolar macrophage complete UP TPM4 7171 Reyman alveolar macrophage complete UP TPP1 1200 Reyman alveolar macrophage complete UP TREM2 54209 Reyman alveolar macrophage complete UP TTYH3 80727 Reyman alveolar macrophage complete UP TUBA1B 10376 Reyman alveolar macrophage complete UP TYMP 1890 Reyman alveolar macrophage complete UP UCP2 7351 Reyman alveolar macrophage complete UP VAMP5 10791 Reyman alveolar macrophage complete UP VMP1 81671 Reyman alveolar macrophage complete UP WARS 7453 Reyman alveolar macrophage complete UP WASF2 10163 Reyman alveolar macrophage complete UP ZFP36L1 677 Reyman alveolar macrophage complete UP

Table of Liao et al Clusters GeneSymbol Cluster ENTREZID S100A9 G1 6280 S100A8 G1 6279 S100A12 G1 6283 VCAN G1 1462 FCN1 G1 2219 CORO1A G1 11151 SELL G1 6402 CD14 G1 929 CFP G1 5199 RNASE2 G1 6036 SERPINB1 G1 1992 FPR1 G1 2357 COTL1 G1 23406 MPEG1 G1 219972 LST1 G1 7940 STAB1 G1 23166 RNASE6 G1 6039 MS4A6A G1 64231 IL1RN G1 & G2 3557 CCL7 G1 & G2 6354 IFITM2 G1 & G2 10581 IFIT2 G1 & G2 3433 PLAC8 G1 & G2 51316 IFIT3 G1 & G2 3437 SERPINB9 G1 & G2 5272 NAMPT G1 & G2 10135 LILRA5 G1 & G2 353514 IER2 G1 & G2 9592 IFITM3 G1 & G2 10410 MX1 G1 & G2 4599 NFKBIA G1 & G2 4792 ANXA2R G1 & G2 389289 RSAD2 G1 & G2 91543 IFIT1 G1 & G2 3434 DUSP6 G1 & G2 1848 ACTB G1 & G2 60 SLC25A37 G2 51312 TNFSF10 G2 8743 CLU G2 1191 CXCL10 G2 3627 APOBEC3A G2 200315 CCL3L1 G2 6349 FFAR2 G2 2867 HSPA6 G2 3310 CCL2 G2 6347 HSPA1A G2 3303 CCL8 G2 6355 DNAJB1 G2 3337 HSPA1B G2 3304 CCL4 G2 6351 CCL3 G2 6348 CCL4L2 G2 9560 HSPB1 G2 3315 IDO1 G2 3620 ISG15 G2 9636 ISG20 G2 3669 TIMP1 G2 7076 NINJ1 G2 4814 VAMP5 G2 10791 CYP1B1 G2 1545 HSPH1 G2 10808 TYMP G2 1890 CXCL11 G2 6373 WARS1 G2 7453 BAG3 G2 9531 GBP1 G2 2633 SOD2 G2 6648 HSP90AA1 G2 3320 BCL2A1 G2 597 GBP5 G2 115362 PLEK G2 5341 NCF1 G2 653361 CALHM6 G2 441168 SLAMF7 G2 57823 SGK1 G2 6446 DEFB1 G2 1672 ANKRD22 G2 118932 GCH1 G2 2643 PLA2G7 G2 7941 CTSB G2 1508 HAMP G3 57817 LGMN G3 5641 RGS1 G3 5996 SPP1 G3 6696 RNASE1 G3 6035 HMOX1 G3 3162 GPR183 G3 1880 ARL4C G3 10123 C1QC G3 714 SDS G3 10993 TGFB1 G3 7040 A2M G3 2 FPR3 G3 2359 CD84 G3 8832 NRP2 G3 8828 CREG1 G3 8804 SDC3 G3 9672 CTSL G3 1514 MMP14 G3 4323 SMPDL3A G3 10924 PMP22 G3 5376 PLD3 G3 23646 LIPA G3 3988 MS4A4A G3 51338 CSF1R G3 1436 CD86 G3 942 GPNMB G3 10457 CREM G3 1390 APOE G3 348 HSP90B1 G3 7184 C1QB G3 713 CCL18 G3 6362 IL7R G3 3575 CXCL8 G3 3576 IFITM1 G3 8519 FABP5 G4 2171 FABP4 G4 2167 NUPR1 G4 26471 APOC1 G4 341 GCHFR G4 2644 INHBA G4 3624 ALOX5AP G4 241 ALDH2 G4 217 CD52 G4 1043 HLA-DQA1 G4 3117 HLA-DQB1 G4 3119 LPL G4 4023 MCEMP1 G4 199675 MARCO G4 8685 TFRC G4 7037 HPGD G4 3248 FBP1 G4 2203 RBP3 G4 5949 ACP5 G4 54 PEBP1 G4 5037 MSR1 G4 4481 MRC1 G4 4360 AKR1C3 G4 8644

Table of PPI Putative Myeloid Population geneSymbol EntrezID Category PLD3 23646 PPI PBMC Myeloid Subcluster 1 NMNAT1 64802 PPI PBMC Myeloid Subcluster 1 CSGALNACT2 55454 PPI PBMC Myeloid Subcluster 1 DSE 29940 PPI PBMC Myeloid Subcluster 1 MLEC 9761 PPI PBMC Myeloid Subcluster 1 DNAJC5 80331 PPI PBMC Myeloid Subcluster 1 ALDH3B1 221 PPI PBMC Myeloid Subcluster 1 AGPAT2 10555 PPI PBMC Myeloid Subcluster 1 QSOX1 5768 PPI PBMC Myeloid Subcluster 1 SLC2A5 6518 PPI PBMC Myeloid Subcluster 1 MFGE8 4240 PPI PBMC Myeloid Subcluster 1 BST1 683 PPI PBMC Myeloid Subcluster 1 VAMP8 8673 PPI PBMC Myeloid Subcluster 1 HVCN1 84329 PPI PBMC Myeloid Subcluster 1 ATP11A 23250 PPI PBMC Myeloid Subcluster 1 IGFBP7 3490 PPI PBMC Myeloid Subcluster 1 F5 2153 PPI PBMC Myeloid Subcluster 1 VCAN 1462 PPI PBMC Myeloid Subcluster 1 CD93 22918 PPI PBMC Myeloid Subcluster 1 LGALS1 3956 PPI PBMC Myeloid Subcluster 1 TIMP1 7076 PPI PBMC Myeloid Subcluster 1 RAB44 401258 PPI PBMC Myeloid Subcluster 1 CLEC4D 338339 PPI PBMC Myeloid Subcluster 1 MERTK 10461 PPI PBMC Myeloid Subcluster 1 GAS6 2621 PPI PBMC Myeloid Subcluster 1 CLEC5A 23601 PPI PBMC Myeloid Subcluster 1 LRP8 7804 PPI PBMC Myeloid Subcluster 1 MCEMP1 199675 PPI PBMC Myeloid Subcluster 1 CLEC12A 160364 PPI PBMC Myeloid Subcluster 1 APOE 348 PPI PBMC Myeloid Subcluster 1 CD36 948 PPI PBMC Myeloid Subcluster 1 PLD1 5337 PPI PBMC Myeloid Subcluster 1 CD33 945 PPI PBMC Myeloid Subcluster 1 LAIR1 3903 PPI PBMC Myeloid Subcluster 1 FSTL3 10272 PPI PBMC Myeloid Subcluster 1 BACE1 23621 PPI PBMC Myeloid Subcluster 1 CST3 1471 PPI PBMC Myeloid Subcluster 1 CYBB 1536 PPI PBMC Myeloid Subcluster 1 NUCB1 4924 PPI PBMC Myeloid Subcluster 1 C3AR1 719 PPI PBMC Myeloid Subcluster 1 APLP2 334 PPI PBMC Myeloid Subcluster 1 APP 351 PPI PBMC Myeloid Subcluster 1 ITGB2 3689 PPI PBMC Myeloid Subcluster 1 ITGAM 3684 PPI PBMC Myeloid Subcluster 1 LAMC1 3915 PPI PBMC Myeloid Subcluster 1 LAMB2 3913 PPI PBMC Myeloid Subcluster 1 PCSK9 255738 PPI PBMC Myeloid Subcluster 1 FN1 2335 PPI PBMC Myeloid Subcluster 1 FAM20C 56975 PPI PBMC Myeloid Subcluster 1 FAM20A 54757 PPI PBMC Myeloid Subcluster 1 CALU 813 PPI PBMC Myeloid Subcluster 1 P4HB 5034 PPI PBMC Myeloid Subcluster 1 PDIA6 10130 PPI PBMC Myeloid Subcluster 1 ATP6V1D 51382 PPI PBMC Myeloid Subcluster 1 LAMTOR2 28956 PPI PBMC Myeloid Subcluster 1 VPS11 55823 PPI PBMC Myeloid Subcluster 3 UBE2L3 7332 PPI PBMC Myeloid Subcluster 3 GPER1 2852 PPI PBMC Myeloid Subcluster 3 S1PR3 1903 PPI PBMC Myeloid Subcluster 3 MT2A 4502 PPI PBMC Myeloid Subcluster 3 HEBP1 50865 PPI PBMC Myeloid Subcluster 3 SAMHD1 25939 PPI PBMC Myeloid Subcluster 3 OPN3 23596 PPI PBMC Myeloid Subcluster 3 GNG5 2787 PPI PBMC Myeloid Subcluster 3 CXCL10 3627 PPI PBMC Myeloid Subcluster 3 TBC1D2 55357 PPI PBMC Myeloid Subcluster 3 IRF5 3663 PPI PBMC Myeloid Subcluster 3 ADORA3 140 PPI PBMC Myeloid Subcluster 3 CCR2 729230 PPI PBMC Myeloid Subcluster 3 IFITM3 10410 PPI PBMC Myeloid Subcluster 3 FPR3 2359 PPI PBMC Myeloid Subcluster 3 IRF8 3394 PPI PBMC Myeloid Subcluster 3 RAB7A 7879 PPI PBMC Myeloid Subcluster 3 CCZ1 51622 PPI PBMC Myeloid Subcluster 3 CCR1 1230 PPI PBMC Myeloid Subcluster 3 IFI35 3430 PPI PBMC Myeloid Subcluster 3 FCGR1B 2210 PPI PBMC Myeloid Subcluster 3 IFI6 2537 PPI PBMC Myeloid Subcluster 3 RSAD2 91543 PPI PBMC Myeloid Subcluster 3 MX1 4599 PPI PBMC Myeloid Subcluster 3 GALK2 2585 PPI PBMC Myeloid Subcluster 4 CTSB 1508 PPI PBMC Myeloid Subcluster 4 CTSL 1514 PPI PBMC Myeloid Subcluster 4 SGMS2 166929 PPI PBMC Myeloid Subcluster 4 METTL7A 25840 PPI PBMC Myeloid Subcluster 4 ASAH1 427 PPI PBMC Myeloid Subcluster 4 MMP17 4326 PPI PBMC Myeloid Subcluster 4 CFP 5199 PPI PBMC Myeloid Subcluster 4 CTSS 1520 PPI PBMC Myeloid Subcluster 4 NIPA2 81614 PPI PBMC Myeloid Subcluster 4 C5 727 PPI PBMC Myeloid Subcluster 4 IDH1 3417 PPI PBMC Myeloid Subcluster 4 LTA4H 4048 PPI PBMC Myeloid Subcluster 4 ALDOA 226 PPI PBMC Myeloid Subcluster 4 CTSD 1509 PPI PBMC Myeloid Subcluster 4 HP 3240 PPI PBMC Myeloid Subcluster 4 CTSH 1512 PPI PBMC Myeloid Subcluster 4 CSTB 1476 PPI PBMC Myeloid Subcluster 4 TIMP2 7077 PPI PBMC Myeloid Subcluster 4 MMP14 4323 PPI PBMC Myeloid Subcluster 4 HLA-DQA1 3117 PPI PBMC Myeloid Subcluster 4 HLA-DRA 3122 PPI PBMC Myeloid Subcluster 4 FCGR1A 2209 PPI PBMC Myeloid Subcluster 4 CYFIP1 23191 PPI PBMC Myeloid Subcluster 4 NACA2 342538 PPI PBMC Myeloid Subcluster 5 NCAPH 23397 PPI PBMC Myeloid Subcluster 5 PER1 5187 PPI PBMC Myeloid Subcluster 5 PPP1R3D 5509 PPI PBMC Myeloid Subcluster 5 TP53BP2 7159 PPI PBMC Myeloid Subcluster 5 CMPK2 129607 PPI PBMC Myeloid Subcluster 5 RCC2 55920 PPI PBMC Myeloid Subcluster 5 MAPRE1 22919 PPI PBMC Myeloid Subcluster 5 NUP37 79023 PPI PBMC Myeloid Subcluster 5 POLQ 10721 PPI PBMC Myeloid Subcluster 5 PPP1CC 5501 PPI PBMC Myeloid Subcluster 5 OAS2 4939 PPI PBMC Myeloid Subcluster 5 OAS3 4940 PPI PBMC Myeloid Subcluster 5 OAS1 4938 PPI PBMC Myeloid Subcluster 5 OASL 8638 PPI PBMC Myeloid Subcluster 5 FEN1 2237 PPI PBMC Myeloid Subcluster 5 PCNA 5111 PPI PBMC Myeloid Subcluster 5 CDT1 81620 PPI PBMC Myeloid Subcluster 5 MCM2 4171 PPI PBMC Myeloid Subcluster 5 CDC6 990 PPI PBMC Myeloid Subcluster 5 ORC1 4998 PPI PBMC Myeloid Subcluster 5 MCM4 4173 PPI PBMC Myeloid Subcluster 5 MARCO 8685 PPI PBMC Myeloid Subcluster 6 CCDC47 57003 PPI PBMC Myeloid Subcluster 6 MPEG1 219972 PPI PBMC Myeloid Subcluster 6 ALOX5 240 PPI PBMC Myeloid Subcluster 6 TLR5 7100 PPI PBMC Myeloid Subcluster 6 IKBKE 9641 PPI PBMC Myeloid Subcluster 6 MRC1 4360 PPI PBMC Myeloid Subcluster 6 C2 717 PPI PBMC Myeloid Subcluster 6 TLR2 7097 PPI PBMC Myeloid Subcluster 6 CD14 929 PPI PBMC Myeloid Subcluster 6 IRAK3 11213 PPI PBMC Myeloid Subcluster 6 IRAK1 3654 PPI PBMC Myeloid Subcluster 6 S100A12 6283 PPI PBMC Myeloid Subcluster 6 TLR4 7099 PPI PBMC Myeloid Subcluster 6 MYD88 4615 PPI PBMC Myeloid Subcluster 6 CD180 4064 PPI PBMC Myeloid Subcluster 6 LY86 9450 PPI PBMC Myeloid Subcluster 6 S100A8 6279 PPI PBMC Myeloid Subcluster 6 S100A9 6280 PPI PBMC Myeloid Subcluster 6 C1QC 714 PPI PBMC Myeloid Subcluster 6 C1QB 713 PPI PBMC Myeloid Subcluster 6 C1QA 712 PPI PBMC Myeloid Subcluster 6 MLKL 197259 PPI PBMC Myeloid Subcluster 13 PTBP2 58155 PPI PBMC Myeloid Subcluster 13 NLRP3 114548 PPI PBMC Myeloid Subcluster 13 CARD16 114769 PPI PBMC Myeloid Subcluster 13 IL18 3606 PPI PBMC Myeloid Subcluster 13 CASP1 834 PPI PBMC Myeloid Subcluster 13 NLRC4 58484 PPI PBMC Myeloid Subcluster 13 NAIP 4671 PPI PBMC Myeloid Subcluster 13 ADRA2A 150 PPI Lung Myeloid Subcluster 1 BCL3 602 PPI Lung Myeloid Subcluster 1 C3AR1 719 PPI Lung Myeloid Subcluster 1 C5AR1 728 PPI Lung Myeloid Subcluster 1 CCL15 6359 PPI Lung Myeloid Subcluster 1 CCL19 6363 PPI Lung Myeloid Subcluster 1 CCL3 6348 PPI Lung Myeloid Subcluster 1 CCL4 6351 PPI Lung Myeloid Subcluster 1 CCR1 1230 PPI Lung Myeloid Subcluster 1 CCRL2 9034 PPI Lung Myeloid Subcluster 1 CMPK2 129607 PPI Lung Myeloid Subcluster 1 CXCL10 3627 PPI Lung Myeloid Subcluster 1 CXCL11 6373 PPI Lung Myeloid Subcluster 1 CXCL16 58191 PPI Lung Myeloid Subcluster 1 CXCR2 3579 PPI Lung Myeloid Subcluster 1 DDX58 23586 PPI Lung Myeloid Subcluster 1 DDX60 55601 PPI Lung Myeloid Subcluster 1 DDX60L 91351 PPI Lung Myeloid Subcluster 1 DRD2 1813 PPI Lung Myeloid Subcluster 1 EIF2AK2 5610 PPI Lung Myeloid Subcluster 1 EPSTI1 94240 PPI Lung Myeloid Subcluster 1 FPR1 2357 PPI Lung Myeloid Subcluster 1 FPR2 2358 PPI Lung Myeloid Subcluster 1 GNG2 54331 PPI Lung Myeloid Subcluster 1 GNG5 2787 PPI Lung Myeloid Subcluster 1 GPR37L1 9283 PPI Lung Myeloid Subcluster 1 GPSM3 63940 PPI Lung Myeloid Subcluster 1 HCAR1 27198 PPI Lung Myeloid Subcluster 1 HCAR2 338442 PPI Lung Myeloid Subcluster 1 HELZ2 85441 PPI Lung Myeloid Subcluster 1 HERC5 51191 PPI Lung Myeloid Subcluster 1 HERC6 55008 PPI Lung Myeloid Subcluster 1 HLA-A 3105 PPI Lung Myeloid Subcluster 1 HLA-B 3106 PPI Lung Myeloid Subcluster 1 HTR1A 3350 PPI Lung Myeloid Subcluster 1 IDO1 3620 PPI Lung Myeloid Subcluster 1 IFI44 10561 PPI Lung Myeloid Subcluster 1 IFI44L 10964 PPI Lung Myeloid Subcluster 1 IFI6 2537 PPI Lung Myeloid Subcluster 1 IFIH1 64135 PPI Lung Myeloid Subcluster 1 IFIT1 3434 PPI Lung Myeloid Subcluster 1 IFIT1B 439996 PPI Lung Myeloid Subcluster 1 IFIT2 3433 PPI Lung Myeloid Subcluster 1 IFIT3 3437 PPI Lung Myeloid Subcluster 1 IFIT5 24138 PPI Lung Myeloid Subcluster 1 IFITM1 8519 PPI Lung Myeloid Subcluster 1 IFITM2 10581 PPI Lung Myeloid Subcluster 1 IFITM3 10410 PPI Lung Myeloid Subcluster 1 IL27 246778 PPI Lung Myeloid Subcluster 1 IRF2 3660 PPI Lung Myeloid Subcluster 1 IRF7 3665 PPI Lung Myeloid Subcluster 1 ISG15 9636 PPI Lung Myeloid Subcluster 1 KCNJ2 3759 PPI Lung Myeloid Subcluster 1 MX1 4599 PPI Lung Myeloid Subcluster 1 MX2 4600 PPI Lung Myeloid Subcluster 1 OAS1 4938 PPI Lung Myeloid Subcluster 1 OAS2 4939 PPI Lung Myeloid Subcluster 1 OAS3 4940 PPI Lung Myeloid Subcluster 1 OASL 8638 PPI Lung Myeloid Subcluster 1 P2RY13 53829 PPI Lung Myeloid Subcluster 1 P2RY14 9934 PPI Lung Myeloid Subcluster 1 RSAD2 91543 PPI Lung Myeloid Subcluster 1 RTP4 64108 PPI Lung Myeloid Subcluster 1 SAA1 6288 PPI Lung Myeloid Subcluster 1 SAMD9 54809 PPI Lung Myeloid Subcluster 1 SAMD9L 219285 PPI Lung Myeloid Subcluster 1 SP110 3431 PPI Lung Myeloid Subcluster 1 STAT1 6772 PPI Lung Myeloid Subcluster 1 STAT2 6773 PPI Lung Myeloid Subcluster 1 SUCNR1 56670 PPI Lung Myeloid Subcluster 1 TNFSF10 8743 PPI Lung Myeloid Subcluster 1 UBE2L6 9246 PPI Lung Myeloid Subcluster 1 USP15 9958 PPI Lung Myeloid Subcluster 1 USP18 11274 PPI Lung Myeloid Subcluster 1 XAF1 54739 PPI Lung Myeloid Subcluster 1 ZBP1 81030 PPI Lung Myeloid Subcluster 1 CCL2 6347 PPI Lung Myeloid Subcluster 2 CCL7 6354 PPI Lung Myeloid Subcluster 2 CDA 978 PPI Lung Myeloid Subcluster 2 CHI3L1 1116 PPI Lung Myeloid Subcluster 2 CHIT1 1118 PPI Lung Myeloid Subcluster 2 CRISP3 10321 PPI Lung Myeloid Subcluster 2 FLG2 388698 PPI Lung Myeloid Subcluster 2 HBB 3043 PPI Lung Myeloid Subcluster 2 HP 3240 PPI Lung Myeloid Subcluster 2 LCN2 3934 PPI Lung Myeloid Subcluster 2 LTF 4057 PPI Lung Myeloid Subcluster 2 MMP8 4317 PPI Lung Myeloid Subcluster 2 PGLYRP1 8993 PPI Lung Myeloid Subcluster 2 TCN1 6947 PPI Lung Myeloid Subcluster 2 MAP2K6 5608 PPI Lung Myeloid Subcluster 8 MCTS1 28985 PPI Lung Myeloid Subcluster 8 PSMA4 5685 PPI Lung Myeloid Subcluster 8 PSME3 10197 PPI Lung Myeloid Subcluster 8 TNF 7124 PPI Lung Myeloid Subcluster 8 TNFSF13B 10673 PPI Lung Myeloid Subcluster 8 TNFSF14 8740 PPI Lung Myeloid Subcluster 8 TP73 7161 PPI Lung Myeloid Subcluster 8 AIM2 9447 PPI Lung Myeloid Subcluster 9 CASP4 837 PPI Lung Myeloid Subcluster 9 CASP5 838 PPI Lung Myeloid Subcluster 9 CASP1 834 PPI Lung Myeloid Subcluster 10 IL1A 3552 PPI Lung Myeloid Subcluster 10 IL1R2 7850 PPI Lung Myeloid Subcluster 10 IL1RN 3557 PPI Lung Myeloid Subcluster 10 ADCYAP1 116 PPI Lung Myeloid Subcluster 3 BST1 683 PPI Lung Myeloid Subcluster 3 CD38 952 PPI Lung Myeloid Subcluster 3 CD53 963 PPI Lung Myeloid Subcluster 3 CEACAM1 634 PPI Lung Myeloid Subcluster 3 CERS6 253782 PPI Lung Myeloid Subcluster 3 CLEC12A 160364 PPI Lung Myeloid Subcluster 3 CLEC12B 387837 PPI Lung Myeloid Subcluster 3 CLEC4D 338339 PPI Lung Myeloid Subcluster 3 CLEC4E 26253 PPI Lung Myeloid Subcluster 3 CYBB 1536 PPI Lung Myeloid Subcluster 3 CYSTM1 84418 PPI Lung Myeloid Subcluster 3 FCER1G 2207 PPI Lung Myeloid Subcluster 3 GPR84 53831 PPI Lung Myeloid Subcluster 3 MGAM 8972 PPI Lung Myeloid Subcluster 3 MS4A3 932 PPI Lung Myeloid Subcluster 3 ALOX5AP 241 PPI Lung Myeloid Subcluster 6 AQP9 366 PPI Lung Myeloid Subcluster 6 ARHGAP9 64333 PPI Lung Myeloid Subcluster 6 C1QB 713 PPI Lung Myeloid Subcluster 6 C2 717 PPI Lung Myeloid Subcluster 6 CAPZA1 829 PPI Lung Myeloid Subcluster 6 CCL18 6362 PPI Lung Myeloid Subcluster 6 CCL8 6355 PPI Lung Myeloid Subcluster 6 CD74 972 PPI Lung Myeloid Subcluster 6 CMTM2 146225 PPI Lung Myeloid Subcluster 6 COL9A2 1298 PPI Lung Myeloid Subcluster 6 CTF1 1489 PPI Lung Myeloid Subcluster 6 EVI2A 2123 PPI Lung Myeloid Subcluster 6 EVI2B 2124 PPI Lung Myeloid Subcluster 6 FCGR2A 2212 PPI Lung Myeloid Subcluster 6 FCN1 2219 PPI Lung Myeloid Subcluster 6 GAPT 202309 PPI Lung Myeloid Subcluster 6 HCST 10870 PPI Lung Myeloid Subcluster 6 IFNL1 282618 PPI Lung Myeloid Subcluster 6 IGLL5 100423062 PPI Lung Myeloid Subcluster 6 IGSF6 10261 PPI Lung Myeloid Subcluster 6 IL2RG 3561 PPI Lung Myeloid Subcluster 6 LILRA1 11024 PPI Lung Myeloid Subcluster 6 LY86 9450 PPI Lung Myeloid Subcluster 6 NCF4 4689 PPI Lung Myeloid Subcluster 6 PIK3AP1 118788 PPI Lung Myeloid Subcluster 6 PLEK 5341 PPI Lung Myeloid Subcluster 6 RAC2 5880 PPI Lung Myeloid Subcluster 6 RNASE2 6036 PPI Lung Myeloid Subcluster 6 S100A12 6283 PPI Lung Myeloid Subcluster 6 S100A8 6279 PPI Lung Myeloid Subcluster 6 S100A9 6280 PPI Lung Myeloid Subcluster 6 SELL 6402 PPI Lung Myeloid Subcluster 6 STX11 8676 PPI Lung Myeloid Subcluster 6 TAGAP 117289 PPI Lung Myeloid Subcluster 6 TFEC 22797 PPI Lung Myeloid Subcluster 6 TLR1 7096 PPI Lung Myeloid Subcluster 6 TMEM176B 28959 PPI Lung Myeloid Subcluster 6 BCL2A1 597 PPI Lung Myeloid Subcluster 4 C1QC 714 PPI Lung Myeloid Subcluster 4 CARD16 114769 PPI Lung Myeloid Subcluster 4 CLEC4A 50856 PPI Lung Myeloid Subcluster 4 CSF2RB 1439 PPI Lung Myeloid Subcluster 4 FGL2 10875 PPI Lung Myeloid Subcluster 4 IL1B 3553 PPI Lung Myeloid Subcluster 4 RGS18 64407 PPI Lung Myeloid Subcluster 4 TLR7 51284 PPI Lung Myeloid Subcluster 4 ARRB2 409 PPI Lung Myeloid Subcluster 7 C6 729 PPI Lung Myeloid Subcluster 7 C8A 731 PPI Lung Myeloid Subcluster 7 CDH2 1000 PPI Lung Myeloid Subcluster 7 EGF 1950 PPI Lung Myeloid Subcluster 7 F5 2153 PPI Lung Myeloid Subcluster 7 FGG 2266 PPI Lung Myeloid Subcluster 7 FGL1 2267 PPI Lung Myeloid Subcluster 7 IGFBP1 3484 PPI Lung Myeloid Subcluster 7 LMAN1L 79748 PPI Lung Myeloid Subcluster 7 LY96 23643 PPI Lung Myeloid Subcluster 7 LYN 4067 PPI Lung Myeloid Subcluster 7 OR13G1 441933 PPI Lung Myeloid Subcluster 7 OR2AT4 341152 PPI Lung Myeloid Subcluster 7 OR2C1 4993 PPI Lung Myeloid Subcluster 7 PCSK9 255738 PPI Lung Myeloid Subcluster 7 RBP4 5950 PPI Lung Myeloid Subcluster 7 SERPINA1 5265 PPI Lung Myeloid Subcluster 7 SERPINE2 5270 PPI Lung Myeloid Subcluster 7 BDKRB2 624 PPI BAL Myeloid Subcluster 2 C3 718 PPI BAL Myeloid Subcluster 2 C3AR1 719 PPI BAL Myeloid Subcluster 2 CCL20 6364 PPI BAL Myeloid Subcluster 2 CCL4 6351 PPI BAL Myeloid Subcluster 2 CCL7 6354 PPI BAL Myeloid Subcluster 2 CCR1 1230 PPI BAL Myeloid Subcluster 2 CCR5 1234 PPI BAL Myeloid Subcluster 2 CXCL1 2919 PPI BAL Myeloid Subcluster 2 CXCL10 3627 PPI BAL Myeloid Subcluster 2 CXCL11 6373 PPI BAL Myeloid Subcluster 2 CXCL12 6387 PPI BAL Myeloid Subcluster 2 CXCL16 58191 PPI BAL Myeloid Subcluster 2 CXCL2 2920 PPI BAL Myeloid Subcluster 2 CXCL3 2921 PPI BAL Myeloid Subcluster 2 CXCL6 6372 PPI BAL Myeloid Subcluster 2 CXCL9 4283 PPI BAL Myeloid Subcluster 2 FPR3 2359 PPI BAL Myeloid Subcluster 2 GNAI1 2770 PPI BAL Myeloid Subcluster 2 GNB4 59345 PPI BAL Myeloid Subcluster 2 GNG12 55970 PPI BAL Myeloid Subcluster 2 GNG5 2787 PPI BAL Myeloid Subcluster 2 GNGT2 2793 PPI BAL Myeloid Subcluster 2 HCAR2 338442 PPI BAL Myeloid Subcluster 2 KCNJ10 3766 PPI BAL Myeloid Subcluster 2 KCNJ16 3773 PPI BAL Myeloid Subcluster 2 KCNJ5 3762 PPI BAL Myeloid Subcluster 2 LPAR1 1902 PPI BAL Myeloid Subcluster 2 LPAR3 23566 PPI BAL Myeloid Subcluster 2 NPW 283869 PPI BAL Myeloid Subcluster 2 PAQR5 54852 PPI BAL Myeloid Subcluster 2 PTGER3 5733 PPI BAL Myeloid Subcluster 2 RGS22 26166 PPI BAL Myeloid Subcluster 2 SAA1 6288 PPI BAL Myeloid Subcluster 2 SSTR2 6752 PPI BAL Myeloid Subcluster 2 SUCNR1 56670 PPI BAL Myeloid Subcluster 2 TAS2R13 50838 PPI BAL Myeloid Subcluster 2 ABI1 10006 PPI BAL Myeloid Subcluster 7 C1QA 712 PPI BAL Myeloid Subcluster 7 C1QB 713 PPI BAL Myeloid Subcluster 7 C1QC 714 PPI BAL Myeloid Subcluster 7 C2 717 PPI BAL Myeloid Subcluster 7 CFH 3075 PPI BAL Myeloid Subcluster 7 CRK 1398 PPI BAL Myeloid Subcluster 7 DOCK1 1793 PPI BAL Myeloid Subcluster 7 FCGR2A 2212 PPI BAL Myeloid Subcluster 7 FCGR3A 2214 PPI BAL Myeloid Subcluster 7 GK 2710 PPI BAL Myeloid Subcluster 7 IGSF6 10261 PPI BAL Myeloid Subcluster 7 KNDC1 85442 PPI BAL Myeloid Subcluster 7 LILRB4 11006 PPI BAL Myeloid Subcluster 7 MARCO 8685 PPI BAL Myeloid Subcluster 7 MRC1 4360 PPI BAL Myeloid Subcluster 7 NCKAP1 10787 PPI BAL Myeloid Subcluster 7 PLA2G7 7941 PPI BAL Myeloid Subcluster 7 ANXA2 302 PPI BAL Myeloid Subcluster 3 APOE 348 PPI BAL Myeloid Subcluster 3 C6 729 PPI BAL Myeloid Subcluster 3 C8B 732 PPI BAL Myeloid Subcluster 3 CD44 960 PPI BAL Myeloid Subcluster 3 CP 1356 PPI BAL Myeloid Subcluster 3 CREG1 8804 PPI BAL Myeloid Subcluster 3 CTSC 1075 PPI BAL Myeloid Subcluster 3 DCP1B 196513 PPI BAL Myeloid Subcluster 3 FABP5 2171 PPI BAL Myeloid Subcluster 3 FCGR1A 2209 PPI BAL Myeloid Subcluster 3 FCGR1B 2210 PPI BAL Myeloid Subcluster 3 FGFR2 2263 PPI BAL Myeloid Subcluster 3 FN1 2335 PPI BAL Myeloid Subcluster 3 FRK 2444 PPI BAL Myeloid Subcluster 3 FTL 2512 PPI BAL Myeloid Subcluster 3 FUCA1 2517 PPI BAL Myeloid Subcluster 3 GBP1 2633 PPI BAL Myeloid Subcluster 3 GBP6 163351 PPI BAL Myeloid Subcluster 3 GM2A 2760 PPI BAL Myeloid Subcluster 3 GOLM1 51280 PPI BAL Myeloid Subcluster 3 HLA-DPA1 3113 PPI BAL Myeloid Subcluster 3 HLA-DQA1 3117 PPI BAL Myeloid Subcluster 3 HLA-DQA2 3118 PPI BAL Myeloid Subcluster 3 HLA-DQB2 3120 PPI BAL Myeloid Subcluster 3 IFI6 2537 PPI BAL Myeloid Subcluster 3 IFIH1 64135 PPI BAL Myeloid Subcluster 3 IFIT3 3437 PPI BAL Myeloid Subcluster 3 IFIT5 24138 PPI BAL Myeloid Subcluster 3 IFITM3 10410 PPI BAL Myeloid Subcluster 3 IGFBP3 3486 PPI BAL Myeloid Subcluster 3 IGFBP5 3488 PPI BAL Myeloid Subcluster 3 IL17RD 54756 PPI BAL Myeloid Subcluster 3 IRF2 3660 PPI BAL Myeloid Subcluster 3 IRF6 3664 PPI BAL Myeloid Subcluster 3 ISG15 9636 PPI BAL Myeloid Subcluster 3 LAMB1 3912 PPI BAL Myeloid Subcluster 3 LGMN 5641 PPI BAL Myeloid Subcluster 3 MGAT4A 11320 PPI BAL Myeloid Subcluster 3 MID1 4281 PPI BAL Myeloid Subcluster 3 MMP1 4312 PPI BAL Myeloid Subcluster 3 MMP10 4319 PPI BAL Myeloid Subcluster 3 MMP7 4316 PPI BAL Myeloid Subcluster 3 MSLN 10232 PPI BAL Myeloid Subcluster 3 MT2A 4502 PPI BAL Myeloid Subcluster 3 NKAP 79576 PPI BAL Myeloid Subcluster 3 OAS1 4938 PPI BAL Myeloid Subcluster 3 OAS2 4939 PPI BAL Myeloid Subcluster 3 OASL 8638 PPI BAL Myeloid Subcluster 3 OSBPL1A 114876 PPI BAL Myeloid Subcluster 3 PDCD1LG2 80380 PPI BAL Myeloid Subcluster 3 PRSS23 11098 PPI BAL Myeloid Subcluster 3 PTRH2 51651 PPI BAL Myeloid Subcluster 3 PYCARD 29108 PPI BAL Myeloid Subcluster 3 S100A2 6273 PPI BAL Myeloid Subcluster 3 S100A7 6278 PPI BAL Myeloid Subcluster 3 SDC2 6383 PPI BAL Myeloid Subcluster 3 SDCBP 6386 PPI BAL Myeloid Subcluster 3 SERPINB3 6317 PPI BAL Myeloid Subcluster 3 SERPINB4 6318 PPI BAL Myeloid Subcluster 3 SP110 3431 PPI BAL Myeloid Subcluster 3 SPARCL1 8404 PPI BAL Myeloid Subcluster 3 SPP1 6696 PPI BAL Myeloid Subcluster 3 TNC 3371 PPI BAL Myeloid Subcluster 3 TRIM14 9830 PPI BAL Myeloid Subcluster 3 TRIM2 23321 PPI BAL Myeloid Subcluster 3 ACACB 32 PPI BAL Myeloid Subcluster 5 ACADM 34 PPI BAL Myeloid Subcluster 5 APOC1 341 PPI BAL Myeloid Subcluster 5 BDP1 55814 PPI BAL Myeloid Subcluster 5 BNIP3 664 PPI BAL Myeloid Subcluster 5 BRD8 10902 PPI BAL Myeloid Subcluster 5 CCL3 6348 PPI BAL Myeloid Subcluster 5 CEBPB 1051 PPI BAL Myeloid Subcluster 5 CEP350 9857 PPI BAL Myeloid Subcluster 5 CNOT1 23019 PPI BAL Myeloid Subcluster 5 DEPTOR 64798 PPI BAL Myeloid Subcluster 5 DHX32 55760 PPI BAL Myeloid Subcluster 5 EIF4EBP1 1978 PPI BAL Myeloid Subcluster 5 FABP4 2167 PPI BAL Myeloid Subcluster 5 FABP6 2172 PPI BAL Myeloid Subcluster 5 FAM120B 84498 PPI BAL Myeloid Subcluster 5 FNIP1 96459 PPI BAL Myeloid Subcluster 5 FNIP2 57600 PPI BAL Myeloid Subcluster 5 GPN3 51184 PPI BAL Myeloid Subcluster 5 GRHL1 29841 PPI BAL Myeloid Subcluster 5 GTF3A 2971 PPI BAL Myeloid Subcluster 5 GTF3C6 112495 PPI BAL Myeloid Subcluster 5 HMGCS2 3158 PPI BAL Myeloid Subcluster 5 ITPA 3704 PPI BAL Myeloid Subcluster 5 KLF5 688 PPI BAL Myeloid Subcluster 5 LAMTOR5 10542 PPI BAL Myeloid Subcluster 5 LEP 3952 PPI BAL Myeloid Subcluster 5 LPL 4023 PPI BAL Myeloid Subcluster 5 MCTS1 28985 PPI BAL Myeloid Subcluster 5 MED11 400569 PPI BAL Myeloid Subcluster 5 MED19 219541 PPI BAL Myeloid Subcluster 5 MED21 9412 PPI BAL Myeloid Subcluster 5 MED7 9443 PPI BAL Myeloid Subcluster 5 MED8 112950 PPI BAL Myeloid Subcluster 5 NCOA2 10499 PPI BAL Myeloid Subcluster 5 NFIA 4774 PPI BAL Myeloid Subcluster 5 NFIB 4781 PPI BAL Myeloid Subcluster 5 NFIC 4782 PPI BAL Myeloid Subcluster 5 NR2F2 7026 PPI BAL Myeloid Subcluster 5 PDE9A 5152 PPI BAL Myeloid Subcluster 5 POLR3B 55703 PPI BAL Myeloid Subcluster 5 POLR3C 10623 PPI BAL Myeloid Subcluster 5 POLR3K 51728 PPI BAL Myeloid Subcluster 5 PPARG 5468 PPI BAL Myeloid Subcluster 5 PPARGC1A 10891 PPI BAL Myeloid Subcluster 5 PRKAA1 5562 PPI BAL Myeloid Subcluster 5 PRKAA2 5563 PPI BAL Myeloid Subcluster 5 PRKAG1 5571 PPI BAL Myeloid Subcluster 5 PRKAG3 53632 PPI BAL Myeloid Subcluster 5 RGL1 23179 PPI BAL Myeloid Subcluster 5 RHEB 6009 PPI BAL Myeloid Subcluster 5 RRAGA 10670 PPI BAL Myeloid Subcluster 5 RRAGB 10325 PPI BAL Myeloid Subcluster 5 RRAGC 64121 PPI BAL Myeloid Subcluster 5 AIM2 9447 PPI BAL Myeloid Subcluster 9 CASP4 837 PPI BAL Myeloid Subcluster 9 CASP5 838 PPI BAL Myeloid Subcluster 9 IFI16 3428 PPI BAL Myeloid Subcluster 9 IL18 3606 PPI BAL Myeloid Subcluster 9 NLRC4 58484 PPI BAL Myeloid Subcluster 9

Co-expressed Myeloid Subpopulations GeneSymbol EntrezID CoV-2 PBMC Myeloid A1 ADAMDEC1 27299 ADGRE2 30817 AIF1 199 AOAH 313 APOBEC3B 9582 APOBR 55911 APOC1 341 BST1 683 C1QA 712 C1QB 713 C1QC 714 C1RL 51279 C2 717 C4A 720 C4B 721 C4BPA 722 C5 727 C6 729 CCL18 6362 CCL2 6347 CCL7 6354 CCL8 6355 CD101 9398 CD14 929 CD163 9332 CD209 30835 CD300C 10871 CD300E 342510 CD300LF 146722 CD33 945 CD68 968 CD80 941 CFD 1675 CFP 5199 CLEC10A 10462 CLEC12A 160364 CLEC12B 387837 CLEC16A 23274 CLEC4A 50856 CLEC4D 338339 CLEC4E 26253 CLEC5A 23601 CLEC6A 93978 CLEC7A 64581 CSF1R 1436 CSF2RA 1438 CSF2RB 1439 CSF3R 1441 CST3 1471 CXCL10 3627 CXCL11 6373 CXCL2 2920 CXCL9 4283 CYBA 1535 CYBB 1536 FCER1G 2207 FCGR1A 2209 FCGR1B 2210 FCGR2A 2212 FCGR2B 2213 FCGR2C 9103 FGR 2268 FLT3 2322 FOLR2 2350 FUT4 2526 GRN 2896 HVCN1 84329 IFI30 10437 IGSF6 10261 IL10RA 3587 IL18 3606 IL1A 3552 IL1RAP 3556 IL1RN 3557 ITGAX 3687 LGALS12 85329 LGALS9 3965 LILRA1 11024 LILRA2 11027 LILRA5 353514 LILRA6 79168 LILRB1 10859 LILRB2 10288 LILRB3 11025 LILRB4 11006 LILRB5 10990 LMNB1 4001 LY86 9450 LYVE1 10894 LYZ 4069 MARCO 8685 MEFV 4210 MERTK 10461 MFGE8 4240 MNDA 4332 MPEG1 219972 MRC1 4360 MS4A4A 51338 MS4A6A 64231 MSR1 4481 NLRP12 91662 NLRP3 114548 NOD2 64127 NTSR1 4923 OSCAR 126014 OTOF 9381 PECAM1 5175 PILRA 29992 PLEK 5341 PRAM1 84106 RNASE3 6037 RNASE6 6039 RNASE7 84659 S100A8 6279 S100A9 6280 SCARB1 949 SECTM1 6398 SEMA4A 64218 SERPINB9 5272 SERPING1 710 SIGLEC1 6614 SIGLEC10 89790 SIGLEC5 8778 SIGLEC7 27036 SKAP2 8935 SLC11A1 6556 SLITRK4 139065 SPI1 6688 TGM2 7052 THBD 7056 TLR2 7097 TLR8 51311 TNF 7124 TNFAIP8L2 79626 TNFRSF1B 7133 TNFSF13B 10673 TREM1 54210 TREML4 285852 TYROBP 7305 UNC93B1 81622 VENTX 27287 VSIG4 11326 VSTM1 284415 CoV-2 Lung Myeloid A2 ADAMDEC1 27299 ADGRE1 2015 ADGRE2 30817 AIF1 199 APOBEC3B 9582 APOBEC3G 60489 APOBR 55911 APOC1 341 BST1 683 C1QA 712 C1QB 713 C1QC 714 C2 717 C4BPA 722 C4BPB 725 C6 729 C8A 731 CCL18 6362 CCL2 6347 CCL22 6367 CCL7 6354 CCL8 6355 CD14 929 CD300E 342510 CD33 945 CD80 941 CFD 1675 CFP 5199 CHI3L1 1116 CHIT1 1118 CLEC12A 160364 CLEC12B 387837 CLEC1A 51267 CLEC2B 9976 CLEC4A 50856 CLEC4D 338339 CLEC4E 26253 CLEC7A 64581 CSF2 1437 CSF2RB 1439 CSF3R 1441 CST3 1471 CXCL1 2919 CXCL10 3627 CXCL11 6373 CXCL13 10563 CXCL8 3576 CXCR2 3579 CYBA 1535 CYBB 1536 FCER1G 2207 FCGR1A 2209 FCGR2A 2212 FCGR2B 2213 FCGR2C 9103 FCGR3A 2214 FCGR3B 2215 FFAR2 2867 FGR 2268 FOLR2 2350 GRN 2896 IFNL1 282618 IGSF6 10261 IL12B 3593 IL18 3606 IL18RAP 8807 IL1A 3552 IL1B 3553 IL1RAP 3556 IL1RN 3557 IL20 50604 IL23A 51561 IL27 246778 ITGAX 3687 LAMP3 27074 LGALS9 3965 LGALS9C 654346 LILRA5 353514 LILRA6 79168 LILRB1 10859 LILRB2 10288 LILRB3 11025 LILRB4 11006 LILRB5 10990 LMNB1 4001 LY86 9450 LYZ 4069 MNDA 4332 MPEG1 219972 MS4A4A 51338 MS4A6A 64231 MSR1 4481 NLRP3 114548 OLR1 4973 OTOF 9381 PDCD1LG2 80380 PILRA 29992 PLEK 5341 S100A8 6279 S100A9 6280 S1PR5 53637 SECTM1 6398 SEMA4A 64218 SERPINB9 5272 SERPING1 710 SIGLEC14 1E+08 SIGLEC5 8778 SLPI 6590 SPI1 6688 TLR2 7097 TNF 7124 TNFSF13B 10673 TNFSF14 8740 TNIP3 79931 TREM1 54210 TREML4 285852 TYROBP 7305 UNC93B1 81622 VSIG4 11326

CoV-2 BAL Lung Myeloid A3 GeneSymbol EntrezID ACE 1636 ADAMDEC1 27299 ADGRE3 84658 AIF1 199 APOBEC3G 60489 APOC1 341 C1QA 712 C1QB 713 C1QC 714 C1R 715 C2 717 C4BPA 722 C5 727 C6 729 CCL18 6362 CCL2 6347 CCL28 56477 CCL7 6354 CCL8 6355 CD163 9332 CD300LF 146722 CD5L 922 CD68 968 CD80 941 CHI3L1 1116 CLEC2B 9976 CLEC4E 26253 CLEC5A 23601 CLEC6A 93978 CXCL1 2919 CXCL10 3627 CXCL11 6373 CXCL2 2920 CXCL8 3576 CXCL9 4283 CXCR2 3579 FCER1G 2207 FCGR1A 2209 FCGR1B 2210 FCGR2A 2212 FCGR2C 9103 FCGR3A 2214 FCGR3B 2215 FOLR2 2350 IGSF6 10261 IK 3550 IL18 3606 IL1A 3552 IL1B 3553 IL1RN 3557 IL23A 51561 LAMP3 27074 LGALS9B 284194 LGALS9C 654346 LILRB4 11006 LILRB5 10990 LY86 9450 LYVE1 10894 MARCO 8685 MERTK 10461 MNDA 4332 MRC1 4360 MS4A4A 51338 MSR1 4481 OLR1 4973 OTOF 9381 PDCD1LG2 80380 PILRA 29992 RNASE7 84659 SCARB1 949 SERPING1 710 SIGLEC1 6614 SIGLEC14 100049587 SIGLEC5 8778 SIGLEC7 27036 SKAP2 8935 SLAMF8 56833 SLPI 6590 STAP2 55620 TGM2 7052 TLR8 51311 TNF 7124 TNFAIP8L2 79626 TNFSF13B 10673 TNIP3 79931 TYROBP 7305 VSIG4 11326

CoV-2 PBMC Myeloid B1 GeneSymbol EntrezID ACE 1636 ADAM8 101 ADGRE1 2015 ADGRE3 84658 APOBEC3G 60489 C1R 715 CCL28 56477 CD5L 922 CHI3L1 1116 CHIT1 1118 CLEC2B 9976 CXCL1 2919 CXCL8 3576 CXCR2 3579 FCER1A 2205 FCGR3A 2214 FCGR3B 2215 FFAR2 2867 IK 3550 IL18RAP 8807 IL1B 3553 IL23A 51561 LAMP3 27074 LGALS9B 284194 LGALS9C 654346 OLR1 4973 PDCD1LG2 80380 PYHIN1 149628 S1PR5 53637 SIGLEC14 1E+08 SLAMF8 56833 SLPI 6590 STAP2 55620 TNFSF14 8740 TNIP3 79931 TREML2 79865

CoV-2 PBMC Lung B2 GeneSymbol EntrezID ACE 1636 ADAM8 101 AOAH 313 ART4 420 BMX 660 C1R 715 C1RL 51279 C4A 720 C4B 721 CD163 9332 CD209 30835 CD300C 10871 CD300LF 146722 CD5L 922 CFB 629 CLEC10A 10462 CLEC16A 23274 CLEC5A 23601 CSF1R 1436 CSF2RA 1438 CXCL2 2920 CXCL9 4283 FCER1A 2205 FCGR1B 2210 FUT4 2526 HVCN1 84329 IK 3550 IL10RA 3587 IL12A 3592 IL31RA 133396 LGALS9B 284194 LILRA1 11024 LILRA2 11027 LYVE1 10894 MARCO 8685 MEFV 4210 MERTK 10461 MFGE8 4240 MRC1 4360 NLRP12 91662 NOD2 64127 OSCAR 126014 PECAM1 5175 PLA2G5 5322 PRAM1 84106 PYHIN1 149628 RNASE6 6039 SCARB1 949 SIGLEC1 6614 SKAP2 8935 SLC11A1 6556 STAP2 55620 TEK 7010 TGM2 7052 THBD 7056 TLR8 51311 TNFAIP8L2 79626 TNFRSF1B 7133

CoV-2 BAL Myeloid B3 GeneSymbol EntrezID ADAM8 101 ADGRE1 2015 ADGRE2 30817 AOAH 313 APOBEC3B 9582 APOBR 55911 BST1 683 C1RL 51279 C4A 720 C4B 721 CD101 9398 CD14 929 CD209 30835 CD300C 10871 CD300E 342510 CD33 945 CFD 1675 CFP 5199 CHIT1 1118 CLEC10A 10462 CLEC12A 160364 CLEC12B 387837 CLEC16A 23274 CLEC4A 50856 CLEC4D 338339 CLEC7A 64581 CSF1R 1436 CSF2RA 1438 CSF2RB 1439 CSF3R 1441 CST3 1471 CYBA 1535 CYBB 1536 FCER1A 2205 FCGR2B 2213 FFAR2 2867 FGR 2268 FLT3 2322 FUT4 2526 GRN 2896 HVCN1 84329 IFI30 10437 IL10RA 3587 IL18RAP 8807 IL1RAP 3556 ITGAX 3687 LGALS12 85329 LGALS9 3965 LILRA1 11024 LILRA2 11027 LILRA5 353514 LILRA6 79168 LILRB1 10859 LILRB2 10288 LILRB3 11025 LMNB1 4001 LYZ 4069 MEFV 4210 MFGE8 4240 MPEG1 219972 MS4A6A 64231 NLRP12 91662 NLRP3 114548 NOD2 64127 NTSR1 4923 OSCAR 126014 PECAM1 5175 PLEK 5341 PRAM1 84106 PYHIN1 149628 RNASE3 6037 RNASE6 6039 S100A8 6279 S100A9 6280 S1PR5 53637 SECTM1 6398 SEMA4A 64218 SERPINB9 5272 SIGLEC10 89790 SLC11A1 6556 SLITRK4 139065 SPI1 6688 THBD 7056 TLR2 7097 TNFRSF1B 7133 TNFSF14 8740 TREM1 54210 TREML2 79865 TREML4 285852 UNC93B1 81622 VENTX 27287 VSTM1 284415

Co-Expressed Myeloid Subpopulations Venn Diagrams

PBMC/Lung/BAL GeneSymbol EntrezID ADAMDEC1 27299 AIF1 199 APOC1 341 C1QA 712 C1QB 713 C1QC 714 C2 717 C4BPA 722 C6 729 CCL18 6362 CCL2 6347 CCL7 6354 CCL8 6355 CD80 941 CLEC4E 26253 CXCL10 3627 CXCL11 6373 FCER1G 2207 FCGR1A 2209 FCGR2A 2212 FCGR2C 9103 FOLR2 2350 IGSF6 10261 IL18 3606 IL1A 3552 IL1RN 3557 LILRB4 11006 LILRB5 10990 LY86 9450 MNDA 4332 MS4A4A 51338 MSR1 4481 OTOF 9381 PILRA 29992 SERPING1 710 SIGLEC5 8778 TNF 7124 TNFSF13B 10673 TYROBP 7305 VSIG4 11326

PBMC/Lung GeneSymbol EntrezID ADGRE2 30817 APOBEC3B 9582 APOBR 55911 BST1 683 CD14 929 CD300E 342510 CD33 945 CFD 1675 CFP 5199 CLEC12A 160364 CLEC12B 387837 CLEC4A 50856 CLEC4D 338339 CLEC7A 64581 CSF2RB 1439 CSF3R 1441 CST3 1471 CYBA 1535 CYBB 1536 FCGR2B 2213 FGR 2268 GRN 2896 IL1RAP 3556 ITGAX 3687 LGALS9 3965 LILRA5 353514 LILRA6 79168 LILRB1 10859 LILRB2 10288 LILRB3 11025 LMNB1 4001 LYZ 4069 MPEG1 219972 MS4A6A 64231 NLRP3 114548 PLEK 5341 S100A8 6279 S100A9 6280 SECTM1 6398 SEMA4A 64218 SERPINB9 5272 SPI1 6688 TLR2 7097 TREM1 54210 TREML4 285852 UNC93B1 81622

PBMC/BAL GeneSymbol EntrezID C5 727 CD163 9332 CD300LF 146722 CD68 968 CLEC5A 23601 CLEC6A 93978 CXCL2 2920 CXCL9 4283 FCGR1B 2210 LYVE1 10894 MARCO 8685 MERTK 10461 MRC1 4360 RNASE7 84659 SCARB1 949 SIGLEC1 6614 SIGLEC7 27036 SKAP2 8935 TGM2 7052 TLR8 51311 TNFAIP8L2 79626

LUNG/BAL GeneSymbol EntrezID APOBEC3G 60489 CHI3L1 1116 CLEC2B 9976 CXCL1 2919 CXCL8 3576 CXCR2 3579 FCGR3A 2214 FCGR3B 2215 IL1B 3553 IL23A 51561 LAMP3 27074 LGALS9C 654346 OLR1 4973 PDCD1LG2 80380 SIGLEC14 1E+08 SLPI 6590 TNIP3 79931

PBMC GeneSymbol EntrezID AOAH 313 C1RL 51279 C4A 720 C4B 721 CD101 9398 CD209 30835 CD300C 10871 CLEC10A 10462 CLEC16A 23274 CSF1R 1436 CSF2RA 1438 FLT3 2322 FUT4 2526 HVCN1 84329 IFI30 10437 IL10RA 3587 LGALS12 85329 LILRA1 11024 LILRA2 11027 MEFV 4210 MFGE8 4240 NLRP12 91662 NOD2 64127 NTSR1 4923 OSCAR 126014 PECAM1 5175 PRAM1 84106 RNASE3 6037 RNASE6 6039 SIGLEC10 89790 SLC11A1 6556 SLITRK4 139065 THBD 7056 TNFRSF1B 7133 VENTX 27287 VSTM1 284415

LUNG GeneSymbol EntrezID ADGRE1 2015 C4BPB 725 C8A 731 CCL22 6367 CHIT1 1118 CLEC1A 51267 CSF2 1437 CXCL13 10563 FFAR2 2867 IFNL1 282618 IL12B 3593 IL18RAP 8807 IL20 50604 IL27 246778 S1PR5 53637 TNFSF14 8740

BAL GeneSymbol EntrezID ACE 1636 ADGRE3 84658 C1R 715 CCL28 56477 CD5L 922 IK 3550 LGALS9B 284194 SLAMF8 56833 STAP2 55620

Example 2: Comprehensive Transcriptomic Analysis of COVID-19 Blood, Lung, and Airway

SARS-CoV2 may refer to an uncharacterized coronavirus and causative agent of the COVID-19 pandemic. The host response to SARS-CoV2 has not yet been fully delineated, hampering a precise approach to therapy. To address this, a comprehensive analysis of gene expression data from the blood, lung, and airway of COVID-19 patients was performed. The results obtained indicate that COVID-19 pathogenesis is driven by populations of myeloid-lineage cells with highly inflammatory but distinct transcriptional signatures in each compartment. The relative absence of cytotoxic cells in the lung indicates a model in which delayed clearance of the virus may permit exaggerated myeloid cell activation that contributes to disease pathogenesis by the production of inflammatory mediators. The gene expression profiles may also identify potential therapeutic targets that may be modified with available drugs. The results and data indicate that transcriptomic profiling can provide an understanding of the pathogenesis of COVID-19 in individual patients.

Coronaviruses (CoV) generally refer to a group of enveloped, single, positive-stranded RNA viruses causing mild to severe respiratory illnesses in humans (Refs. 1-3). In the past two decades, three worldwide outbreaks have originated from CoVs capable of infecting the lower respiratory tract, resulting in heightened pathogenicity and high mortality rates. There is currently a global pandemic stemming from a third CoV strain, severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the causative agent of coronavirus disease 2019 (COVID-19). In the majority of cases, patients exhibit mild symptoms, whereas in more severe cases, patients may develop severe lung injury and death from respiratory failure (Refs. 4-5).

At this time, there is still incomplete information available regarding the host response to SARS-CoV2 infection and the perturbations resulting in a severe outcome. Despite this, clues can be derived from our knowledge of the immune response to infection by other respiratory viruses, including other CoVs. After infection, viruses are typically detected by pattern recognition receptors (PRRs) such as the inflammasome sensor NLRP3, which signal the release of interferons (IFNs) and inflammatory cytokines including the IL-1 family, IL-6, and TNF, that activate a local and systemic response to infection (Refs. 6-7). This involves the recruitment, activation, and differentiation of innate and adaptive immune cells, including neutrophils, inflammatory myeloid cells, CD8 T cells, and natural killer (NK) cells (Ref 8). Resolution of infection may be largely dependent on the cytotoxic activity of CD8 T cells and NK cells, which enable clearance of virus-infected cells (Ref 8). Failure to clear virus-infected cells may facilitate a hyper-inflammatory state termed Macrophage (M1) activation syndrome (MAS) or “cytokine storm”, and ultimately damage to the infected lung (Refs. 9-10).

The recent emergence of SARS-CoV2 and the relative lack of comprehensive knowledge regarding the progression of COVID-19 disease has constrained the ability to develop effective treatments for infected patients. One approach to obtain a more complete understanding of the host response to SARS-CoV2 is to examine gene expression in relevant tissues. A limited number of gene expression profiles may be available from patients with COVID-19 and have yielded some insights into the pathogenic processes triggered by infection with SARS-CoV2 (Refs. 11-13). However, because of the small number of samples and limited analysis, a comprehensive understanding of the biological state of SARS-CoV2-affected tissues may not be available. Recognizing this need, the present disclosure provides an analysis and assessment of available SARS-CoV2 gene expression datasets from blood, lung, and airway using a number of orthogonal bioinformatic tools to provide a more complete view of the nature of the COVID-19 inflammatory response and the potential points of therapeutic intervention.

Gene expression analysis of blood, lung, and airway of COVID-19 patients was performed as follows. To characterize the pathologic response to SARS-CoV2 infection, transcriptomic data was analyzed from peripheral blood mononuclear cells (PBMCs) and postmortem lung tissue of COVID-19 patients and healthy controls as well as bronchoalveolar lavage (BAL) fluid of COVID-19 patients (CRA002390, GSE147507, FIGS. 25A-25D) (Refs. 11-12). First, changes in gene expression were determined in the blood (PBMC-CTL vs PBMC-CoV2) and lung (Lung-CTL vs Lung-CoV2). Because no control BAL fluids were associated with the BAL-CoV2 samples, BAL-CoV2 was compared to PBMC-CoV2 from the same dataset to avoid effects related to batch and methodology. Overall, a set of 4,245 differentially expressed genes (DEGs) in the blood (2,166 up and 2,079 down), 2,220 DEGs in the lung (684 up and 1,536 down), and 8,952 DEGs in the airway (BAL) (4,052 up and 4,900 down) were determined (Table 6).

Conserved and differential enrichment of inflammatory cells and pathways in COVID-19 patients was analyzed as follows. To interrogate pathologic pathways in the 3 compartments, Gene Set Variation Analysis (GSVA) was performed utilizing a number of informative gene modules (Refs. 14-15) (FIG. 17 ). Numerous innate immune response pathways were increased in all 3 compartments, whereas adaptive immune signatures tended to be decreased in blood and airway, but not lung (Refs. 11-12 and 16). Although heterogeneity was observed in all compartments, closer examination revealed consistent perturbations. In the blood, the classical and lectin-induced complement pathways, as well as the NLRP3 inflammasome, plasma cells (PCs), and monocytes (Mo) were significantly enriched in COVID-19 patients, whereas cytotoxic cells and neutrophils were decreased. In the lung, the NLRP3 inflammasome, Mo and myeloid cells were enriched in COVID-19 patients. In addition, although the general granulocyte signature was not significantly increased, a specific low-density granulocyte (LDG) signature (Ref 17) and gene sets of inflammatory and suppressive neutrophils derived from COVID-19 blood were enriched in the lung (Refs. 18-19). In the airway, the classical and alternative complement pathways were enriched and T cells and cytotoxic cells were decreased.

Although there is conflicting data on the presence of an IFN gene signature (IGS) and whether SARS-CoV2 infection induces a robust IFN response (Refs. 12-13 and 20), increased expression was observed of Type I IFN genes (IFNA4, IFNA6, IFNA10), and significant enrichment was observed of the common Type I and Type II IGS, including enrichment of IFNA2, IFNB1 and IFNG gene signatures specifically in the lung tissue (FIGS. 18A-18B). Furthermore, increased expression was detected of genes found to be important for the anti-viral innate immune response (IFIH1, DDX58, EIF2AK2, OAS2), and decreased expression was detected of negative regulators of this response (IRF2BP1, SKIV2L) in both the lung and airway compartments (FIG. 18C) (Ref 21). Interestingly, expression of MAVS, a signaling adaptor for RNA virus sensors, was observed to be decreased in the airway, which is consistent with the reported effect of SARS-CoV2 and may reflect a mechanism of viral immune evasion (Refs. 22-23).

Increased expression of inflammatory mediators in the lungs of COVID-19 patients was analyzed as follows. To examine the nature of the inflammatory response in the tissue compartments in greater detail, specific DEGs of interest (FIG. 19 , sections a and b) were examined. In the blood, increased expression was observed of the inflammatory chemokine CXCL10, which is an IFNG response gene and involved in the activation and chemotaxis of peripheral immune cells, (Ref 24), the chemokine receptor CCR2, which may be critical for immune cell recruitment in response to respiratory viral infection (Ref 25), as well as the inflammatory IL-1 family member, IL18. Expression of a number of chemokines, including ligands for CCR2, were significantly increased in both the lung tissue and airway of COVID-19 patients, including CCL2, CCL3L1, CCL7, CCL8, and CXCL10. Elevated pro-inflammatory IL-1 family members, ILIA and IL1B, were also observed in these 2 compartments. Furthermore, lung tissue exhibited enrichment of the IL-1 cytokine gene signature, whereas the airway exhibited additional expression of IL18, IL33, IL36B, and IL36G.

It was observed that non-hematopoietic cells in the BAL fluid may be indicative of viral-induced damage, as follows. To determine whether viral infection resulted in modification of resident tissue populations, GSVA was performed with various non-hematopoietic cell gene signatures (FIG. 19C). It was observed that signatures of various lung tissue cells but not endothelial cells were enriched in the airway, but not the lung of COVID-19 subjects. Additionally, increased expression was detected of the viral entry genes ACE2 and TMPRSS2, which are typically expressed on lung epithelium (Ref. 26) (FIG. 19D).

It was observed that protein-protein interactions identify myeloid subsets in COVID-19 patients, as follows. An unbiased, protein-protein interaction (PPI)-based clustering approach was utilized to assess the inflammatory cell types within each tissue compartment. PPI networks predicted from DEGs were simplified into metastructures defined by the number of genes in each cluster, the number of significant intra-cluster connections, and the number of associations connecting members of different clusters to each other (FIG. 20A-20C). Overall, upregulated PPI networks identified numerous specific cell types and functions. In the blood, cluster 8 was dominated by a Mo population expressing C2, C5, CXCL10, CCR2, and multiple IFN-stimulated genes, whereas cluster 3 contained hallmarks of alternatively activated (M2) MΦs and/or myeloid-derived suppressor cells (MDSCs), including CD33, CD36, CD93, and ITGAM (FIG. 20A). Smaller immune clusters were indicative of functions, including inflammasome activation, damage-associated molecular pattern (DAMP) activity, the classical complement cascade and the response to Type II IFNs. Myeloid heterogeneity in the blood was also reflected by the presence of multiple metabolic pathways, such as enhanced oxidative phosphorylation (OXPHOS) in cluster 1 linked to M2-like MΦs in cluster 3 (mean interaction score of 0.875), and glycolysis in clusters 7 and 13 connected to activated Mo in cluster 8 (interaction scores of 0.86 and 0.82, respectively). Consistent with our GSVA results, blood exhibited profoundly decreased T cells determined by the downregulation of T cell activation markers CD28, LCK and ITK (FIG. 17 , section a).

In addition to the various Mo/myeloid populations, lung tissue was infiltrated by LDGs, granulocytes, T cells, and B cells. Metabolic function in the lung was varied, with Mo-enriched clusters (1 and 7) linked to glycolysis in cluster 18 (interaction scores of 0.74 and 0.87, respectively) potentially reflecting cellular activation, whereas OXPHOS was predominantly downregulated along with other nuclear processes (transcription and mRNA processing) (FIG. 20B; FIG. 17 , section b). The airway was enriched in inflammatory Mo, mitochondrial function and transcription. Multifunctional cluster 4 was dominated by numerous chemokine and cytokine receptor-ligand pairs, whereas smaller immune clusters were enriched in classical complement activation, IFNG and IL-1 responses. (FIG. 20C). Consistent with tissue damage, numerous small clusters were observed in the airway, reflecting the presence of non-hematopoietic cells, including those containing multiple intermediate filament keratin genes, cell-cell adhesion claudin genes and surfactant genes. Notably, non-hematopoietic cell signatures in the airway were similar in content to those derived from in vitro SARS-CoV-2-infected primary lung epithelial cell lines (NHBE) (Ref. 12) (FIG. 17 , section d).

Given the large number of clusters including Mo/myeloid/MΦ, next these clusters were examined in greater detail by altering the stringency of PPI clustering to further characterize unique myeloid lineage cells within each tissue compartment (FIG. 20D-20F). Myeloid lineage-specific clusters were then compared to pre-determined gene signatures, including populations G1-G4 reported in BAL of COVID-19 patients (Ref. 27) (FIG. 18A). In the blood, gene modules representative of common myeloid function (chemotaxis, proteolysis, etc.), as well as two independent Mo/myeloid subpopulations (FIG. 20D), were detected. Cluster 6 contained numerous markers highly reminiscent of classically activated blood Mo and exhibited significant overlap with the inflammatory G1 population, whereas cluster 1 was similar to IFN-activated MΦs, CX3CR1+ synovial lining MΦs (from arthritic mice) and alveolar MΦs (AM) (FIG. 18A).

In the lung (FIG. 20E), clusters 2, 3, and 6 overlapped with the G1 inflammatory Mo population and expressed a number of chemotaxis genes. A second population characteristic of AMs was also evident in the lung, defined by CSF2RB, the receptor for GM-CSF, a cytokine that regulates AM differentiation (Refs. 8 and 28-29). Further characterization of this population indicated significant expression of the coagulation system genes F5, FGG, FGL1, SERPINA, and SERPINE2. Similarly, re-clustering of Mo/MΦs/myeloid clusters from the airway revealed a population with hallmarks of inflammatory/M1 MΦ (MARCO and multiple members of the complement cascade; cluster 7), and a second population of AMs (FIG. 20F) demonstrating significant overlap with the G3 and G4 populations (FIG. 18A) (Ref. 27).

Characterization of myeloid populations in COVID-19 patients was performed as follows. The overlap between characterized BAL-defined gene signatures from COVID-19 patients (Ref. 27) and tissue-defined PPI clusters motivated an evaluation of these populations in greater detail by GSVA. Consistent with PPI clusters, the inflammatory-MΦ G1 population was increased in the blood (FIG. 18B). The G1 and G1 & G2 populations were increased in the lung, consistent with the expression of IFN and pro-inflammatory cytokines (FIG. 18C). In the airway, the G2, G3, and G4 populations were significantly enriched indicating the presence of both pro-inflammatory MΦs and AMs (FIGS. 18A-18C). As a whole, it was found that gene signatures of defined Mo/MΦ populations in COVID-19 BAL were dispersed among the blood, lung, and airway compartment.

It was observed that co-expression further delineates Mo/MΦ gene expression profiles of COVID-19 patients, as follows. Next, the biology of the populations of Mo/MΦ in the tissue compartments were examined in greater detail. A set of 196 co-expressed Mo/myeloid genes was derived and used (FIG. 19 , Tables 7A-7C) to probe heterogeneity in each tissue compartment (FIG. 21A). Notably, co-expression of 40 core genes was observed between all compartments, which included complement, chemokine, and cytokine genes (FIG. 21B). In addition, there were 86 shared co-expressed genes in lung and blood, 57 in the lung and airway, and 61 in the airway and blood (FIG. 21B). To directly compare levels of these 196 co-expressed myeloid genes in each compartment, gene expression was normalized in each sample using 3 genes included in the core 40 genes, (FCGR1A, FCGR2A, FCGR2C) (FIG. 21C). Although many genes were not significantly different between compartments, numerous chemokines and cell surface markers (CCL2, CCL7, CCL8, CXCL10, CLEC4E, FCER1G) and inflammatory cytokines (IL1A and TNF) were enriched in the lung compared to the blood and airway. Furthermore, the complement genes C1QB, C1QC, and C2 were increased in the lung compared to the blood, but not changed between the lung and the airway. Altogether, these normalized gene expression results indicated that expression of inflammatory mediators was increased in SARS-CoV2-infected lung over the other compartments and in the airway compared to the blood.

To determine the function and nature of these myeloid populations, they were compared to other myeloid signatures (FIG. 21D) (Refs. 27 and 30-33). The population increased in the blood (A1) was predominantly characterized by features of AMs, M1 and M2 MΦs, pro-inflammatory MΦs with potential to infiltrate tissue, and the inflammatory MΦ G1 population. The A1 population also exhibited features of inflamed murine residential, interstitial MΦs. The myeloid cell population increased in COVID lung (A2) was most similar to pro-fibrotic AMs, M1 MΦs, M2 MΦs, blood-derived infiltrating MΦs, and the inflammatory Mo G1 population. A2 was also marked by additional AM-specific genes, contributing to the observed overlap with the other two compartments. However, overlap between A2 and the G4 AM signature was relatively decreased, suggesting that the lung AMs are more similar to those found in pulmonary fibrosis (Ref 30). Finally, the population increased in the airway (A3) similarly exhibited characteristics of AMs, M1 and M2 MΦs, and pro-inflammatory MΦs that have infiltrated into the tissue compartment (FIG. 21D). Of note, the airway A3 population was not similar to the BAL-derived inflammatory MΦ G1 population (Ref. 27).

Also, the overlap between the Mo/MΦ A1-A3 gene clusters and those identified using PPI clustering (FIGS. 20A-20F; FIG. 21E) was evaluated. Interestingly, the CD33+ pathogenic population (PPI-derived PBMC Myeloid Cluster 1) was most strongly enriched in the blood, but was also increased in the other compartments. All compartments were characterized by strong enrichment of pro-inflammatory Mo (PBMC Myeloid Cluster 6, Lung Myeloid Clusters 3 and 6, and BAL Myeloid Cluster 7), although A3 exhibited some differences in these populations compared to A1 and A2. Additionally, this comparison suggested enrichment of AMs in all three compartments; however, upon examination of the specific overlapping gene transcripts, the observed enrichment in blood A1 was primarily related to the presence of non-AM-specific myeloid genes. Finally, numerous common activators and functions of PPI-derived clusters were enriched uniformly across A1, A2, and A3, providing further evidence for pro-inflammatory activity of myeloid cell populations in COVID-19 blood and tissue compartments.

Trajectory analysis was performed to understand potential transitions of Mo/MΦ in various tissue compartments. This was based on the normalized 196 myeloid-cell specific genes, as well as 425 additional normalized genes that may be important in Mo/myeloid/MΦ cell differentiation, reflective of chemotaxis, IFN, and metabolism genes. This analysis suggested a branch point of differentiation of Mo/MΦ between blood and lung, with some blood Mo/MΦ differentiating directly to airway cells and others to lung cells in a more protracted manner as indicated by pseudotime (FIG. 21F).

Analysis of the biologic activities of myeloid subpopulations was performed as follows. To focus on functional distinctions among the co-expressed myeloid populations in the blood, lung, and airway compartments (A1-A3), linear regression analyses were utilized between GSVA scores for A1-A3 and scores for metabolic, functional, and signaling pathways (FIG. 22 ; FIGS. 20A-20F). Blood A1 was significantly correlated with glycolysis, the NLRP3 inflammasome, and the classical and lectin-induced complement pathways. In lung A2, there were no significant correlations detected with metabolism, but this population was significantly correlated with the NLRP3 inflammasome and the alternative complement pathway. Finally, airway A3 was positively correlated with OXPHOS, the classical complement pathway, and TNF signaling and negatively correlated with apoptosis. Overall, these results delineated the heterogeneity in metabolic and inflammatory pathways among myeloid cells enriched in the blood, lung, and airway of COVID-19 patients.

It was observed that pathway and upstream regulator analysis inform tissue-specific drug discovery for treatment of COVID-19, as follows. To understand the biology of SARS-CoV2-infected patients in greater detail, pathway analysis was conducted on DEGs from the 3 compartments using IPA canonical signaling pathway and upstream regulator (UPR) analysis functions (FIGS. 23A-23B). In general, IFN signaling, the inflammasome, and other components of anti-viral, innate immunity were reflected by disease state gene expression profiles compared to healthy controls (FIG. 23A). In addition, metabolic pathways including OXPHOS and glycolysis were significantly increased in the blood of COVID-19 patients compared to controls.

UPRs predicted to drive the responses in each compartment indicated uniform involvement of inflammatory cytokines, with Type I IFN regulation dominant in the SARS-CoV2-infected lung (FIG. 23B). Notable UPRs of COVID-19 blood included IFNA, IFNG, multiple growth factors and ligands, HIF1A, CSF1 and CSF2. Evidence of inflammatory cytokine signaling by IL17 and IL36A was predicted in COVID-19 lung and airway compartments. Whereas the airway DEG profile indicated regulation by both inflammatory and inhibitory cytokines, the COVID-19 lung UPRs were markedly inflammatory, including, NFκB, IL12, TNF, IL1B, and multiple Type I IFNs. These proinflammatory drivers were consistent in each individual lung which were analyzed separately because of the apparent heterogeneity between the lung samples (FIGS. 21A-21F).

IPA analysis was also employed to predict drugs that might interfere with COVID-19 inflammation (FIG. 23B, Tables 8A-8B). Of note, neutralizers of IL17, IL6, IL1, IFNA, IFNG, and TNF were predicted as antagonists of COVID-19 biology. Corticosteroids were predicted to revert the gene expression profile in the SARS-CoV-2-infected lung, but were predicted as UPRs of COVID-19 blood, which may indicate that the patients from whom blood was collected had been treated with corticosteroids rather than indicating that these agents were driving disease pathology. Chloroquine (CQ) and hydroxychloroquine (HCQ) were additionally predicted to revert the COVID-19 transcription profile in the lung, which may point to their potential utility as treatment options. A number of drugs matched to unique targetable pathways in the lung, including NFκB pathway inhibitors and neutralizers of the TNF family; however, some drugs also targeted pathways shared by both the lung and airway, including JAK inhibitors. In the BAL-CoV2 vs. PBMC-CoV2 IPA comparison, several drugs were matched to UPRs with a negative Z-score, which provided additional therapeutic options directed towards the blood of patients with COVID-19, given that molecules targeting downregulated or inhibited UPRs are molecules that could normalize the PBMC-CoV2 gene signature. As such, several possible therapeutics arose from this analysis to target COVID-19 blood, including ustekinumab, targeting the IL12/23 signaling pathway, and lenalidomide, which have immunosuppressive effects. In addition, IGF1R inhibitors, EGFR inhibitors, VEGFR inhibitors, and AKT inhibitors were among the compounds predicted to target COVID-19 PBMCs. No specific drugs were predicted to target all three tissue compartments, but each compartment was driven by inflammatory cytokines.

Another approach to predict possible drug targets is by employing connectivity scoring with drug-related gene expression profiles using the perturbagen CMAP database within CLUE (Tables 8A-8B). Although CLUE-predicted drugs tended to differ from those predicted by IPA or those matched to IPA-predicted UPRs, there were some overlapping mechanisms, including inhibition of AKT, angiogenesis, CDK, EGFR, FLT3, HSP, JAK, and mTOR. IPA-predicted drugs that were unique from connectivity-predicted drugs tended to capture more cytokine and lymphocyte biology, including inhibitors of IL1, IL6, IL17, TNF, type I and II interferon, CD40LG, CD38, and CD19, among other cytokines and immune cell-specific markers. Overall, the gene expression-based analysis of SARS-CoV2-infected blood and tissue compartments indicated several existing treatment options that may be evaluated as candidates to treat COVID-19, and subsequently administered to patients having COVID-19.

Multiple orthogonal bioinformatics approaches were employed to analyze DEG profiles from the blood, lung, and airway of COVID-19 patients, and revealed the dynamic nature of the inflammatory response to SARS-CoV-2 and possible points of therapeutic intervention. In the blood, evidence was seen of myeloid cell activation, lymphopenia, and elevation of plasma cells, as has been shown by both standard cell counts, flow cytometry and gene expression analysis (Ref 34). In the lungs, increased gene signatures were found of additional myeloid cell types including granulocytes, infiltrating inflammatory Mo, and AMs as well as the presence of non-activated T, B, and NK cells. Furthermore, inflammation in the lung tissue was enhanced by the greater presence of IFNs and more pro-inflammatory cytokines than observed in the blood. Finally, in the airway evidence was found of blood and AM-derived inflammatory and regulatory MΦs, and non-hematopoietic lung tissue cells accompanied by expression of SARS-CoV-2 receptors, and alarmins, indicative of viral infection and damage to the lung and consistent with detection of SARS-CoV2 in BAL fluid (Refs. 11 and 35). Together these findings indicate a systemic, but compartmentalized immune and inflammatory response with specific signs of cellular activation in blood, lung, and airway. This has informed a more comprehensive and integrated model of the nature of the local and systemic host response to SARS-CoV2.

The predominant populations of immune cells found to be enriched and activated in COVID-19 patients were myeloid cells and, in particular, subsets of inflammatory Mo and MΦs, which differed between the blood, lung, and airway compartments. In the peripheral blood, significant enrichment of Mo was found, including classically activated inflammatory M1 MΦs as well as a CD33+ myeloid subset, which appeared to be an M2 population reminiscent of characterized IFN-activated MΦs, AMs, and MDSCs, indicative of a potential regulatory population induced by stimuli arising from the SARS-CoV2-infected lung. Myeloid cells enriched in the blood of COVID-19 patients were also highly correlated with gene signatures of metabolic pathways (Glycolysis, Pentose Phosphate Pathway, and TCA cycle) indicative of pro-inflammatory M1 MΦs (Ref. 36).

The lung tissue was enriched in gene signatures of Mo/MΦs as well as other myeloid cells including two populations of granulocytes, neutrophils and LDGs. Increases in blood neutrophils may be associated with poor disease outcome in COVID-19 patients, and the formation of neutrophil extracellular traps (NETs) may contribute to increased risk of death from SARS-CoV2 infection (Refs. 37-39). In addition, populations of dysregulated neutrophils expressing pro-inflammatory or suppressive markers derived from scRNA-seq of COVID-19 patient PBMCs may be characterized and found to be positively correlated with disease severity (Refs. 18-19). These populations were found to be also increased in SARS-CoV2 infected lung tissue and, therefore, indicate that they may contribute to lung pathology. Although LDGs have not been reported in the COVID-19 lung, in comparison to neutrophils, they exhibit an enhanced capacity to produce Type I IFNs and form NETs and therefore, may have an even greater impact on disease progression (Ref 40).

Mo/MΦ subsets in the lung of COVID-19 patients were characterized as infiltrating inflammatory Mo and activated AMs, which exhibited a mixed metabolic status suggestive of different states of activation. Infiltrating Mo from the peripheral blood appeared to be further activated in the lung tissue as evidenced by enhanced expression of markers of highly inflammatory Mo characterized in severe COVID-19 cases (Ref 27). The AM population enriched in COVID lung tissue clustered with genes involved in the coagulation system, which is consistent with observations of procoagulant AM activity in COVID-19 and in ARDS (Ref. 41). As pulmonary thrombosis has been associated with poor clinical outcomes in COVID-19 patients, this result indicates that activated AMs in SARS-CoV2-infected lung tissue may be involved in facilitating a pro-thrombotic status, and thereby, contribute to poor disease outcome (Ref 42). Finally, a trend was noted toward an increase in platelets specifically in the COVID-19 lung, indicating that they may also contribute to thrombosis in some patients.

In the airway, gene signatures were detected of various post-activated MΦ subsets including inflammatory M1 MΦs, alternatively activated M2 MΦs, and activated AMs. Expression of myeloid cell genes in the airway also correlated with a signature of oxidative metabolism, which is characteristic of M2 macrophages and typically associated with control of tissue damage (Ref. 36). However, in the context of pulmonary infection, polarization of AMs toward an anti-inflammatory M2 phenotype was found to promote continued inflammation, suggesting that these MΦs may not be effective at resolving anti-viral immunity (Ref. 43).

In addition to myeloid cells, inflammatory mediators from the virally infected lung typically promote migration and activation of NK cells and adaptive immune cells including T and B cells (Ref 8). Significant deficiencies were found in gene signatures of T cells and cytotoxic CD8 and NK cells, consistent with clinical evidence of lymphopenia in the peripheral blood and airway of COVID-19 patients (Refs. 44-47). In contrast to T and NK cells, increased evidence was observed of B cell activation through CD40/CD40L and an increased plasma cell signature in the blood of COVID-19 patients. This result indicates that COVID-19 patients are able to mount an antibody-mediated immune response. However, whether a virus-specific antibody response is beneficial to recovery from SARS-CoV2 infection may be unclear (Ref. 48). Low quality, low affinity antibody responses to SARS-CoV may promote lung injury in some patients, although it may be unknown if this occurs in SARS-CoV2 infected individuals (Refs. 49-50).

The contents of the airway as assessed through the BAL fluid, act as a window into events in the alveoli and airways and can be used to understand what is happening in the infected tissue that is separate from the interstitium of the lung (Refs. 51-52). Increased enrichment was found of lung epithelial cells in the airway of COVID-19 patients, indicating that SARS-CoV2 infection of alveolar cells together with localized inflammation as a result of enhanced myeloid cell infiltration promote significant damage to the alveoli and result in affected cells being sloughed into the airway. Furthermore, the lack of cytotoxic cells and thus, the inability to clear these virus-infected lung epithelial cells in the airway likely accounts for the increased presence of post-activated MΦs and high expression of pro-inflammatory IL-1 family members observed in the BAL of COVID-19 patients. Importantly, these results indicate that sampling of BAL may provide an important mechanism to evaluate the impact of SARS-CoV2 infection.

DEGs from COVID-19 patients were enriched in IGS, complement pathways, inflammatory cytokines and the inflammasome, which may be expected to activate Mo/MΦ populations in the blood, lung, and airway of COVID-19 patients and initiate a robust and systemic response to infection. In particular, these results indicate that IL-1 family-mediated inflammation plays a critical role in COVID-19 pathogenesis. However, pro-inflammatory genes identified via GWAS as contributing to COVID-19 inflammation, including CCR2, CCR3, CXCR6, and MTA2B, were not significantly different from controls in the lung dataset (Ref 53). Thus, in contrast to characterizations of both SARS-CoV and SARS-CoV2 infection, these analyses did not indicate the presence of overwhelming pro-inflammatory cytokine production or “cytokine storm” in COVID-19 patients (Refs. 34 and 54). Rather, these data indicates that the increased numbers, overactivation, and potentially heightened pathogenicity of monocyte/MΦ populations are the main drivers of the dysregulated inflammatory response and resulting tissue damage in COVID-19 patients.

In the absence of proven antiviral treatment and/or a SARS-CoV2-specific vaccine, disease management may be reliant upon supportive care and therapeutics capable of limiting the severity of clinical manifestations. Using empiric evidence as a guide, the current approach may be successful in identifying “actionable” points of intervention in an unbiased manner and in spite of formidable patient heterogeneity. Analyses presented here support COVID-19 infection-related increases in inflammatory cytokines, particularly IL6 and TNF, both of which function as predictors of poor prognosis (Refs. 55-56), as well as complement activation (Refs. 37 and 57-58). Accordingly, anti-IL6 therapies including sarilumab, tocilizumab and clazakizumab, as well as biologics targeting terminal components of the complement cascade, such as eculizumab and ravulizumab, are in various clinical trial phases for treating COVID associated pneumonia. Candidate TNF blockers such as adalimumab, etanercept and many others, represent additional options for inhibiting deleterious pro-inflammatory signaling. However, most showed patient heterogeneity, indicating a requirement to identify the specific cytokine profile in each patient in order to offer personalized treatment. Our analyses also indicate the likely involvement of pro-inflammatory IL1 family members especially in the lung, suggesting anti-IL1 family interventions, including canakinumab and anakinra, may be effective in preventing acute lung injury.

This analysis also establishes the predominance of inflammatory Mo/myeloid lineage cells in driving disease pathology and indicates therapies effective at blocking myeloid cell recruitment or forcing repolarization may prevent disease progression. CCL5 (RANTES) is a potent leukocyte chemoattractant that interacts with multiple receptors, including CCR1 (upregulated in the blood, lung and airway), and CCR5 (upregulated in the airway). Disruption of the CCR5-CCL5 axis may be tested using the CCR5 neutralizing monoclonal antibody leronlimab in a compassionate use trial (Ref 59).

It may be observed that COVID-19 may predispose patients to thromboembolic disease (Refs. 60-61). Indeed, the gene expression analyses presented here showing altered expression of coagulation factors and fibrinogen genes indicate dysfunction within the intrinsic clotting pathway. These findings, together with evidence of excessive inflammation, complement activation and the involvement of LDGs in lung inflammation, may contribute to the systemic coagulation underlying the remarkably high incidence of thrombotic complications observed in severely ill patients, thereby reinforcing recommendations to apply pharmacological anti-thrombotic medications.

Further, anti-rheumatic drugs may be used for managing COVID-19. For example, CQ is a compound predicted as a UPR with potential phenotype-reversing properties. In vitro experiments examining the anti-viral properties of CQ and its derivative HCQ were effective in limiting viral load; however, the efficacy of these drugs in clinical trials has been less clear (Ref. 62). Questions about drug timing, dosage and adverse events may call into question the use of these drugs for COVID-19 patients. Despite results showing no negative connectivity between the gene signatures of SARS-CoV2 infection and HCQ treatment (Ref. 35), IPA predicted a role of anti-malarials as limiting the function of intracellular TLRs in the lung and also as a direct negative UPR of gene expression abnormalities in the lung, indicating a role in controlling COVID-19 inflammation and not viral replication. Further clinical testing may be performed to establish this possible utility; subsequently, these anti-malarials may be administered to COVID-19 patients to treat disease.

By comparing the transcriptomic profile of the blood, lung, and airway in COVID-19 patients, a model of the systemic pathogenic response to SARS-CoV2 infection has emerged (FIG. 24 ). SARS-CoV2 infection leads to systemic Mo/MΦ activation, likely as a result of the release of pro-inflammatory mediators from infected cells. Infiltration of immune cells into the lung tissue and alveolus, in particular, neutrophils, LDGs, and pathogenic Mo/MΦ populations promotes a cycle of inflammatory mediator release and further myeloid cell activation, which exacerbates inflammation in the lung and leads to tissue damage. The local release of complement components and clotting factors by infiltrating Mo/MΦ may contribute to both inflammation and thrombotic events. As disease progresses, increased infiltration of pro-inflammatory immune cells, release of inflammatory mediators, and damage to the infected alveolus is reflected by the presence of Mo/MΦ cells and lung epithelial cells in the airway (Ref 51). Furthermore, evidence of both Mo-derived inflammatory MΦs and AMs in the airway compartment indicates that myeloid cell populations from both the blood and the lung tissue are present in the BAL. The accumulation of virus-infected cells and release of alarmins in the airway may not only reflect ongoing infection, but also promote inflammation and prevent resolution of the infection and foster the continuation of the innate immune response. Therefore, sampling the BAL fluid is an effective strategy to monitor tissue inflammation and damage in COVID-19 patients.

As SARS-CoV2 continues to propagate, viral clearance may be impaired by a lack of cytotoxic CD8 T cells and NK cells. This is consistent with MAS occurring in other settings, in which defects in cytotoxic activity of CD8 T cells and NK cells result in enhanced innate immune cell activation and intensified production of pro-inflammatory cytokines, many of which were also expressed in COVID-19 patients (Refs. 9-10). Thus, the results indicated that the lack of activated CD8 T cells and NK cells and subsequent failure to clear virus-infected cells, is a major contributor to the MΦ-driven pathologic response to SARS-CoV2 observed in COVID-19 patients.

In order to develop a model of SARS-CoV2 infection, multiple orthogonal approaches were utilized to analyze gene expression from COVID-19 patients. Heterogeneity among patients in any given cohort may have an increased impact on the overall outcome. One possible reason for this intra-cohort heterogeneity is that the patients may have exhibited varying levels of disease severity. Therefore, additional studies may be performed on more patients, such as by accounting for differences in demographic information and disease status, in order to increase the power of downstream analyses.

As shown, transcriptomic analysis has contributed critical insights into the pathogenesis of COVID-19. Diffuse Mo/MΦ activation is the likely primary driver of clinical pathology. Therefore, this work provides a rationale for placing greater focus on the detrimental effects of exaggerated activation of pathogenic Mo/MΦs and for targeting these populations as an effective treatment strategy for COVID-19 patients.

Ethics statement: publicly available data sets used in this study are listed in Table 5. For each dataset, all patient samples were collected in adherence to local regulations and after obtaining institutional review board approved informed consent. The study corresponding to accession number CRA002309 was approved by the Ethics Committee of the Zhongnan Hospital of Wuhan University. The study corresponding to accession number GSE147505 was approved by the institutional review board at the Icahn School of Medicine at Mount Sinai under protocol HS #12-00145.

Read quality, trimming, mapping and summarization were performed as follows. RNA-seq data were processed using a consistent workflow using FASTQC, Trimmomatic, STAR, Sambamba, and featureCounts. As described below SRA files were downloaded and converted into FASTQ format using SRA toolkit. Read ends and adapters were trimmed with Trimmomatic (version 0.38) using a sliding window, ilmnclip, and headcrop filters. Both datasets were head cropped at 6 bp and adapters were removed before read alignment. Reads were mapped to the human reference genome hg38 using STAR, and the .sam files were converted to sorted .bam files using Sambamba. Read counts were summarized using the featureCounts function of the Subread package (version 1.61).

The RNA-seq tools are all free, open source programs, as follows: SRA toolkit (github.com/ncbi/sra-tools); FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/); Trimmomatic (www.usadellab.org/cms/?page=trimmomatic); STAR (github.com/alexdobin/STAR); labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR.posix/doc/STARmanual.pdf; Sambamba (lomereiter.github.io/sambamba/); and FeatureCounts (subread.sourceforge.net).

Differential gene expression and gene set enrichment analysis were performed as follows. The DESeq2 workflow was used for differential expression analysis. Comparisons were made between control PBMCs and PBMCs from COVID-19 patients (PBMC-CTL vs. PBMC-CoV2) and control lung tissue and lung tissue from COVID-19 patients (Lung-CTL vs. Lung-CoV2). Since no corresponding control BAL samples were available for the COVID-19 BAL samples, BAL samples were compared from COVID-19 patients to COVID-19 PBMC (PBMC-CoV2 vs BAL-CoV2). This was possible because these samples were analyzed on the same platform, run at the same time. Also, normal BAL were compared to BAL of asthmatic individuals to identify genes unrelated to COVID-19 (PRJNA434133).

Two technical replicates were included for BAL cohort, and 4 technical replicates were included for postmortem lung samples. The replicates were collapsed and averaged into one using collapsereplicates function from DESeq2 package. The genes with low expression (i.e genes with very few reads) were removed by filtration. The filtered raw counts were normalized using the DESeq method and differentially expressed genes were determined by FDR<0.2 (Ref 63). Counts were then log 2 transformed and used for downstream analyses (Table 6).

Gene Set Variation Analysis (GSVA) was performed as follows. The GSVA (version 1.25.0) software package (Ref. 64) is an open source package available from R/Bioconductor and was used as a non-parametric, unsupervised method for estimating the variation of pre-defined gene sets in patient and control samples of microarray and RNA-seq expression data sets (www.bioconductor.org/packages/release/bioc/html/GSVA.html). The inputs for the GSVA algorithm were a gene expression matrix of log 2 expression values for pre-defined gene sets. All genes within a gene set were evaluated if the interquartile range (IQR) of their expression across the samples was greater than 0. Enrichment scores (GSVA scores) were calculated non-parametrically using a Kolmogorov Smirnoff (KS)-like random walk statistic and a negative value for a particular sample and gene set, indicating that the gene set has a lower expression than the same gene set with a positive value. The enrichment scores (ES) were the largest positive and negative random walk deviations from zero, respectively, for a particular sample and gene set. The positive and negative ES for a particular gene set depend on the expression levels of the genes that form the pre-defined gene set. GSVA calculates enrichment scores using the log 2 expression values for a group of genes in each SARS-CoV2 patient and healthy control and normalizes these scores between −1 (no enrichment) and +1 (enriched). Welch's t-test was used to calculate the significance of the gene sets between the cohorts. Significant enrichment of gene sets was determined by p-value <0.05.

Derivation of GSVA Gene Sets was performed as follows. Cellular and inflammatory modules and IFN-induced gene sets were derived (Refs. 14-15). Additional inflammatory pathways (NLRP3 Inflammasome, Classical Complement, Alternative Complement, and Lectin-induced Complement were curated from the Molecular Signatures Database. Other signatures were derived (Refs. 27, 30-33, and 65).

Additional hematopoietic cellular gene signatures (monocyte, myeloid, and neutrophil) were derived from I-Scope, a tool developed to identify immune cell specific genes in big data gene expression analyses. Non-hematopoietic fibroblast and lung cell gene sets were derived from T-Scope, a tool developed to identify genes specific for 45 non-hematopoietic cell types or tissues in big gene expression datasets. The T-Scope database contains 1,234 transcripts derived initially from 10,000 tissue enriched and 8,000 cell line enriched genes listed in the Human Protein Atlas. From the list of 18,000 potential tissue or cell specific genes, housekeeping genes and genes differentially expressed in 40 hematopoietic cell datasets were removed. The final gene lists were checked against available single cell analyses to confirm cellular specificity.

Nine single-cell RNA-seq lung cell populations (AT1, AT2, Ciliated, Club, Endothelial, Fibroblasts, Immuno Monocytes, Immuno T Cells, and Lymphatic Endothelium) were downloaded from the Eils Lung Tissues set (Ref. 66) accessed by the UC Santa Cruz Genome Browser (eils-lung.cells.ucsc.edu). Genes occurring in more than one cell type were removed. Additionally, genes known to be expressed by immune cells were removed. The Eils Lung Tissues set Immuno Monocyte, Immuno T Cell, Fibroblast, and Lymphatic Endothelium categories were not employed in further analyses.

Apoptosis and NFkB gene signatures were derived and modified from Ingenuity Pathway Analysis pathways Apoptosis Signaling and NFkB Signaling. ROS-protection was derived from Biologically Informed Gene-Clustering (BIG-C).

Network analysis and visualization were performed as follows. Visualization of protein-protein interaction and relationships between genes within datasets was done using Cytoscape (version 3.6.1) software. STRING (version 1.3.2) generated networks were imported into Cytoscape (version 3.6.1) and partitioned with MCODE via the clusterMaker2 (version 1.2.1) plugin. For PPIs in FIGS. 20A-20C, STRING settings were adjusted to high confidence (0.7), for PPIs in FIGS. 20D-20F, settings were relaxed to medium confidence (0.4). All PPIs were generated without the neighborhood or textmining features. For some PPIs, the average interaction strength using STRING-based cumulative interaction scores was used to determine the strength of interaction between clusters.

Functional and cellular enrichment analysis was performed as follows. Functional enrichment of clusters was performed using Biologically Informed Gene-Clustering (BIG-C), which was developed to understand the potential biological meaning of large lists of genes (Ref 67). Genes are clustered into 53 categories based on their most likely biological function and/or cellular localization based on information from multiple on-line tools and databases including UniProtKB/Swiss-Prot, GO terms, KEGG Pathways, MGI database, NCBI PubMed, and the Interactome. Hematopoietic cellular enrichment was performed using I-Scope, a tool developed to identify immune cell specific genes in big data gene expression analyses. Statistically significant enriched types of cell types in DEGs were determined by Fisher's Exact test overlap p-value and then determining an Odds Ratio of enrichment.

Derivation of co-expressed myeloid subpopulations in each compartment was performed as follows. Co-expression analyses were conducted in R. Sample (control and patient) log 2 expression values for each gene of the 221 identified monocyte/myeloid cell genes in were analyzed for their Pearson correlation coefficient in each tissue compartment (blood, lung, and airway) using the Cor function. Of note, only 196 of 221 genes had changes in gene expression in at least one tissue by RNA-seq. Pearson correlations for these 196 genes were hierarchically clustered by their Euclidian distance into 2 clusters (k=2) using the heatmap.2 function in R. This resulted in 2 Mo/myeloid co-expressed clusters in each compartment corresponding to increased and decreased gene sets. The upregulated co-expressed genes were used to define the A1, A2, and A3 myeloid subpopulations from the blood, lung, and airway compartments, respectively (Tables 7A-7C). The co-expressed myeloid populations in each compartment (A1-A3) were then evaluated for enrichment by GSVA.

Inter-compartment myeloid gene comparisons were performed as follows. To compare relative expression of the 196 myeloid-specific genes among compartments, HTS filtered log 2 expression values for each gene were normalized to the average expression of FCGR1A, FCGR2A, and FCGR2C in each sample. Welch's t-test was used to calculate the significant differences in normalized gene expression between cohorts. Effect sizes were computed between cohorts using the cohen.d function with Hedges' correction in R.

Monocle analyses were performed as follows. Trajectory analyses were performed with Monocle (Refs. 68-70) version 2.14.0 in R. Gene expression values for 621 genes related to myeloid cell differentiation and function including cell surface and secreted markers, M1 and M2 markers, metabolism, and IFN genes were selected as a curated input list (Tables 7A-7C). The HTS filtered log 2 expression values for each of these genes in each sample for each tissue type (PBMC-CoV2, Lung-CoV2, and BAL-CoV2) was normalized by the average log 2 expression of FCGR1A, FCGR2A, and FCGR2C in that particular sample as described above. Normalized expression of these genes was used as the input expression data for Monocle. The CellDataSet was created with parameters of lowerDetectionLimit=0.01 and expressionFamily=uninormal( ). Dimensions were reduced using the DDRTree method, and the max_components parameter was set to 2. Cell state was ordered based upon the state corresponding to PBMC-CoV2.

Linear Regression Analysis was performed as follows. Simple linear regression between calculated myeloid subpopulation A1, A2, and A3 GSVA scores and biological functions or signaling pathway GSVA scores was performed in GraphPad Prism Version 8.4.2. In all analyses where pathway genes (e.g. classical complement) were also myeloid cell genes, these genes were removed from the myeloid GSVA score for that comparison and kept in the pathway GSVA score. For each regression analysis, the Goodness of Fit is displayed as the R squared value and the p-value testing the significant of the slope is displayed. All p-values are displayed with 3 digits and rounded-up unless rounding changes significance.

Ingenuity Pathway Analysis (IPA) was performed as follows. The canonical pathway and upstream regulator functions of IPA core expression analysis tool (Qiagen) were used to interrogate DEG lists. Canonical pathways and upstream regulators were considered significant if |Activation Z-Score|≥2 and overlap p-value <0.01. Chemical reagents, chemical toxicants, and endogenous non-mammalian ligands were culled from all upstream regulator analyses.

Drug-Target Matching was performed as follows. IPA-predicted upstream regulators were annotated with respective targeting drugs and compounds to elucidate potential useful therapies in SARS-CoV2. Drugs targeting gene products of interest by both direct and indirect targeting mechanisms were sourced by Combined Lupus Treatment Scoring (CoLTS)-scored drugs (Ref 71), the Connectivity Map via the drug repurposing tool, DrugBank, and literature mining. Similar methods were employed to determine information about drugs and compounds, including mechanism of action and stage of clinical development. The drug repurposing tool was accessed at clue.io/repurposing-app.

Analysis of COVID-19 PBMC, Lung, and BAL DEG profiles via CLUE was performed as follows. DEGs from PBMC-CoV2 vs. PBMC-CTL, Lung-CoV2 vs. Lung-CTL, and BAL-CoV2 vs. PBMC-CoV2 were used as input for the CMaP and LINCS Unified Environment (CLUE) cloud-based connectivity map analysis platform (clue.io/connectopedia/). Top upregulated and downregulated DEGs from each signature as determined by magnitude of log 2 fold change were sequentially entered into CLUE until 150 of each were accepted for analysis to determine drugs, compounds, small molecules, and other perturbagens that mimic or oppose the uploaded COVID-19 gene expression signatures. Resultant drugs and compounds with negative connectivity scores in the [−75, −100] range were analyzed to include results with high confidence of antagonizing COVID-19 gene expression profiles.

Data Availability: the datasets analyzed in this study are available from the China National Center for Bioinformation's National Genomics Data Center, bigd.big.ac.cn/gsa/browse/CRA002390, and in the NCBI GEO repository www.ncbi.nlm.nih.gov/bioproject/PRJNA615032. Additional data generated or analyzed during this study are described by, for example, Daamen et al., “Comprehensive transcriptomic analysis of COVID-19 blood, lung, and airway”, Scientific Reports, Vol. 11, No. 7052 (2021), which is incorporated by reference herein in its entirety.

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FIG. 17 shows conserved and differential enrichment of immune cells and pathways in blood, lung, and airway of SARS-CoV2-infected patients. (sections a-d) Individual sample gene expression from the blood (section a), lung (section b), and airway (section c) was analyzed by GSVA for enrichment of immune cell and inflammatory pathways. The corresponding heatmap was generated using the R Bioconductor package complexHeatmap (v2.5.6) (Ref 72). Select enrichment scores are shown as violin plots in (section d) generated using GraphPad Prism v8.4.2 (www.graphpad.com). *p<0.05, **p<0.01.

FIGS. 18A-18C show elevated IFN expression in the lung tissue of COVID-19 patients. FIG. 18A: Normalized log 2 fold change RNA-seq expression values for IFN-associated genes from blood, lung, and airway of individual COVID-19 patients. The dotted line represents the expression of each gene in healthy individuals (for blood and lung) or PBMCs from COVID-19 patients (airway). FIG. 18B: Individual sample gene expression from the blood, lung, and airway was analyzed by GSVA for enrichment of IFN-related gene signatures. FIG. 18C: Normalized log 2 fold change RNA-seq expression values for anti-viral genes as in (section a). Generated using GraphPad Prism v8.4.2 (www.graphpad.com). #p<0.2, ##p<0.1, *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001

FIGS. 19A-19D show that viral entry gene expression correlates with enhanced expression of inflammatory mediators in SARS-CoV2-infected lungs. FIGS. 19A-19B: Normalized log 2 fold change RNA-seq expression values for chemokines and chemokine receptors (section a) and IL-1 family members (FIG. 19B) from blood, lung, and airway of COVID-19 patients as in FIG. 18A. FIG. 19C: Individual sample gene expression from the blood, lung, and airway was analyzed by GSVA for enrichment of various lung tissue cell categories. FIG. 19D: Normalized log 2 fold change RNA-seq expression values for viral entry genes as in FIGS. 19A-19B. Generated using GraphPad Prism v8.4.2 (www.graphpad.com). #p<0.2, ##p<0.1, *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001

FIGS. 20A-20F show that PPI analysis identifies different myeloid cell subsets and metabolic pathways in blood, lung, and airway of COVID-19 patients. DE upregulated genes from blood (FIG. 20A), lung (FIG. 20B), and airway (FIG. 20C) were used to create PPI metaclusters using Cytoscape (version 3.6.1) and the clusterMaker2 (version 1.2.1) plugin (Ref. 73). Size indicates the number of genes per cluster, color indicates the number of intra-cluster connections and edge weight indicates the number of inter-cluster connections. Enrichment for biological function and immune cell type was determined by BIG-C and I-Scope, respectively. Small clusters (˜14 genes) with similar function are grouped in dotted-line boxes. Clusters enriched in Mo/myeloid genes were combined by decreasing cluster stringency to create a new set of myeloid-derived metastructures from the blood (FIG. 20D), lung (FIG. 20E), and airway (FIG. 20F). Interaction scores showing the strength of interaction between clusters are indicated (0.4-0.6, medium interaction; 0.61-0.8, strong interaction; 0.81-0.99, very strong interaction).

FIGS. 21A-21F show that different co-expression-derived myeloid populations are found in blood, lung, and airway of COVID-19 patients. (FIG. 21A) GSVA enrichment of myeloid subpopulations increased in COVID-19 blood (A1), lung (A2), and airway (A3). (FIG. 21B) Venn Diagram of the gene overlap between myeloid subpopulations A1-A3. (FIG. 21C) Comparison of normalized log 2 fold change expression values of genes defining A1-A3. Expression values for each sample in each comparison were normalized by the mean of the log 2 fold change expression of FCGR1A, FCGR2A, and FCGR2C. Significant comparisons are displayed by Hedge's G effect size. (FIGS. 21D-21E) Characterization of A1-A3 by enrichment of myeloid populations (FIG. 21D) and PBMC, lung, and BAL myeloid metaclusters from FIGS. 20D-20F (FIG. 21E). Fisher's Exact Test was used to calculate overlap between transcriptomic signatures and significant overlaps (p<0.05) are shown as the negative logarithm of the p-value. (FIG. 21F) Trajectory analysis using expression of 621 genes (196 myeloid-specific genes used in a,b+425 additional myeloid genes shown in Tables 7A-7C) in the blood, lung, and airway compartments. Colors represent sample identity and size represents pseudotime distance along the trajectory. Generated using GraphPad Prism v8.4.2 (www.graphpad.com) and the R package Monocle v2.14.0 68-70.

FIG. 22 shows an analysis of biological activities of myeloid subpopulations. Linear regression between GSVA scores for each of the tissue-specific myeloid populations (A1-A3) and metabolism, NLRP3 Inflammasome, complement, apoptosis, and TNF signaling. Generated using GraphPad Prism v8.4.2 (www.graphpad.com).

FIGS. 23A-23B show a pathway analysis of SARS-CoV-2 blood, lung, and airway. DEGs from each SARS-CoV-2 blood or tissue pairwise comparison were uploaded into IPA (Qiagen Inc., www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis) and canonical signaling pathway (FIG. 23A) and upstream regulator (FIG. 23B) analyses were performed. Heatmaps represent significant results by Activation Z-Score |≥2| and overlap p-value<0.01. The boxes with the dotted outline separate drugs that were predicted as upstream regulators from pathway molecules and complexes. The remaining, significant upstream regulators were matched with drugs with known antagonistic targeting mechanisms. The top 150 UPRs in the lung are shown in (FIG. 23B) and the remaining are in FIGS. 29A-29E. Specific drugs for particular drug families (e.g., Anti-IL17) are found in Tables 8A-8B.

†: FDA-approved

‡: Drug in development/clinical trials

FIG. 24 shows a graphical model of COVID-19 pathogenesis. Proposed model of the inflammatory response to SARS-CoV2 infection in three compartments: the blood, lung, and airway generated using Microsoft PowerPoint version 19.0 and Adobe Illustrator version 25.0.

FIGS. 25A-25D show that metaclusters identify differentially expressed cell populations and functional gene clusters in SARS-CoV2 infected tissues and cell lines. Downregulated DE genes from peripheral blood (FIG. 25A), lung (FIG. 25B), and airway (FIG. 25C), and up-regulated DE genes from the NHBE primary lung epithelial cell line (FIG. 25D) were used to create metaclusters. Metaclusters were generated based on PPI networks, clustered using MCODE and visualized in Cytoscape as in FIGS. 20A-20F. Size indicates the number of genes per cluster, color indicates the number of intra-cluster connections and edge weight indicates the number of inter-cluster connections. Cluster enrichment for biological function and immune cell type was determined by BIG-C and I-Scope, respectively.

FIGS. 26A-26F show an evaluation of macrophage gene signatures in myeloid-derived clusters from COVID-affected blood, lung and BAL fluid. Macrophage signatures from the indicated sources were compared to myeloid clusters from FIGS. 19A-19D. Heatmap depicts signatures with significant overlap (−log (p-value)>1.33) with myeloid clusters from the blood, lung and airway compartments generated using GraphPad Prism v8.4.2 (www.graphpad.com). N/A, non-applicable/non-significant overlap detected. R & D Systems provided signatures for the M1, M2a, M2b, M2c and M2d populations.

FIG. 27 shows heterogeneous expression of monocyte/myeloid cell genes in different CoV2 tissue compartments as compared to control. Evaluation of differential expression of 171 monocyte/myeloid genes in each compartment reveals shared and disparate expression among the tissues. PBMC represents PBMC-CoV2 to PBMC-CTL. Lung represents Lung-CoV2 to Lung-CTL. BAL represents BAL-CoV2 to PBMC-CoV2. Scale bar presents Log 2 Fold Change. N/A represents genes that were not significantly DE at FDR<0.2. Heatmaps generated using GraphPad Prism v8.4.2 (www.graphpad.com).

FIG. 28 shows an analysis of biological activities of myeloid subpopulations. Linear regression between GSVA scores for each of the tissue-specific myeloid populations and metabolic pathways, inlammasome, complement pathways, NFκB complex signaling and ROS protection. Generated using GraphPad Prism v8.4.2 (www.graphpad.com).

FIGS. 29A-29E show a pathway analysis of SARS-CoV-2 lung tissue. FIG. 29A: Remaining significant upstream regulators operative in SARS-CoV-2 lung tissue predicted by IPA upstream regulator analysis. Upstream regulator analysis was also conducted on DEGs from each individual COVID-19 lung compared to healthy controls due to observed heterogeneity FIG. 29B: significant results displayed for Lung1-CoV2 vs. Lung-CTL. FIG. 29C: significant results displayed for Lung2-CoV2 vs. Lung-CTL. Chemical reagents, chemical toxicants, and non-mammalian endogenous chemicals were culled from results. The boxes with the dotted outline separate small molecules/drugs/compounds that were predicted as upstream regulators from pathway molecules and complexes. FIGS. 29D-29E: IPA canonical signaling pathway analysis was conducted on individual COVID-19 lung samples. Pathways and upstream regulators were considered significant by |Activation Z-Score|≥2 and overlap p-value <0.01.

TABLE 5 Summary of datasets used RNA- seq Dataset Accessibility Metadata Method CRA002309 bigd.big.ac.cn/gsa/ 3 PBMC Illumina browse/CRA002390 SARS- NovaSeq CoV-2 5000 3 PBMC healthy donor 3 BALF SARS- CoV-2 GSE147505 www.ncbi.nlm.nih.gov/ 2 Illumina bioproject/PRJNA615032 postmortem NextSeq lung 500 2 healthy lung General COVID Patient/Sample Information Sample Age Collection and Dataset Cohort Gender (years) Isolation CRA002309 PBMC CoV2 3 Males 25-74 PBMC were isolated using Ficoll density gradient method PBMC CTL 3 Unknown Unknown Gender BAL CoV2 3 Males 25-74 BAL fluid was retrieved by gentle syringe suction using sterile saline GSE147505 Lung CoV2 2 Males >60 Acquired post- mortem as fixed lung samples Lung CTL 2 Males >70 Acquired from biopsies of uninfected lungs obtained post- surgery

TABLE 6 (DEGs in Blood, Lung, and Airway) PBMC-CoV2 to PBMC-CTL (4,245 DEGs in Blood) A2M, AAGAB, AAK1, AAMP, AAR2, ABCA2, ABCA3, ABCA5, ABCA6, ABCA7, ABCB1, ABCB7, ABCC2, ABCD1, ABHD15, ABHD17A, ABHD6, ABI2, ABITRAM, ABLIM1, ABRACL, ABT1, ACAA2, ACACB, ACAD10, ACADSB, ACADVL, ACAP1, ACCS, ACD, ACER3, ACHE, ACLY, ACO2, ACOT2, ACOT8, ACOT9, ACOX3, ACP2, ACP5, ACSL3, ACSS2, ACTA1, ACTB, ACTG1, ACTR1A, ACTR1B, ACTR2, ACTR5, ACVRIB, ACVRIC, ACVR2B, ACVRL1, ACYP1, ADA2, ADAM15, ADAM19, ADAM22, ADAM23, ADAM8, ADAM9, ADAMTS10, ADAMTS17, ADAMTS2, ADAMTS4, ADAMTSL5, ADAP2, ADARB1, ADGRB2, ADGRE3, ADGRE5, ADGRG1, ADGRG5, ADGRL1, ADGRL2, ADH5, ADIPOR1, ADORA2A, ADORA3, ADPGK, ADPRH, ADRM1, AEBP2, AFAP1, AFMID, AGAP1, AGAP2, AGAP9, AGBL3, AGFG1, AGFG2, AGK, AGL, AGPAT2, AGPAT3, AGRN, AGTRAP, AHCY, AHCYL1, AHDC1, AIF1, AIFM1, AIMP2, AJM1, AK2, AK4, AK5, AKAP12, AKAP17A, AKAP5, AKAP9, AKIP1, AKNA, AKR1A1, AKR1C3, AKT3, ALAD, ALAS1, ALCAM, ALDH1A1, ALDH1L2, ALDH2, ALDH3A2, ALDH3B1, ALDH4A1, ALDH9A1, ALDOA, ALG1, ALG14, ALG8, ALKBH4, ALOX15, ALOX15B, ALOX5, ALPL, ALS2CL, AMD1, AMDHD2, AMIGO1, AMIGO2, AMMECR1, AMN, AMOT, AMPD2, AMPH, ANAPC15, ANG, ANGPTL6, ANK1, ANK3, ANKLE1, ANKMY1, ANKRA2, ANKRD11, ANKRD12, ANKRD22, ANKRD34A, ANKRD34B, ANKRD36, ANKRD36B, ANKRD36C, ANKRD37, ANKRD39, ANKRD44, ANKRD46, ANKRD49, ANKRD50, ANKRD52, ANKRD54, ANKRD55, ANKS3, ANKS6, ANKZF1, ANLN, ANO10, ANO5, ANO9, ANXA2, ANXA4, ANXA5, ANXA7, AOAH, AOC2, AOC3, AP1B1, AP1S1, AP2M1, AP2S1, AP3M1, AP3M2, AP3S1, AP4S1, APBA3, APBB1, APC2, APEX2, APH1A, API5, APLP2, APMAP, APOE, APOL4, APOLD1, APP, ARCN1, AREG, ARF1, ARF4, ARGLU1, ARHGAP12, ARHGAP15, ARHGAP18, ARHGAP23, ARHGAP24, ARHGAP25, ARHGAP29, ARHGAP31, ARHGAP33, ARHGAP4, ARHGAP5, ARHGAP9, ARHGEF1, ARHGEF11, ARHGEF18, ARHGEF19, ARHGEF3, ARHGEF35, ARHGEF5, ARHGEF9, ARID3B, ARID4A, ARID4B, ARID5B, ARL10, ARL11, ARL4A, ARL4C, ARL6, ARL6IP1, ARL8B, ARMC2, ARMH3, ARMT1, ARNT, ARNTL2, ARPC1B, ARPC3, ARPC5, ARPIN, ARRDC3, ARRDC4, ARSA, ARSB, ARV1, ARVCF, ASAH1, ASAH2B, ASB13, ASCL2, ASGR1, ASGR2, ASH2L, ASL, ASPH, ASPM, ASPRV1, ASTE1, ATAD3B, ATF4, ATF7, ATG12, ATG16L1, ATG2A, ATG3, ATG4A, ATG7, ATG9B, ATM, ATN1, ATP10D, ATP11A, ATP1B3, ATP23, ATP2A2, ATP2A3, ATP2B1, ATP2B4, ATP5F1A, ATP5F1B, ATP5F1C, ATP5F1E, ATP5MC1, ATP5MC2, ATP5MC3, ATP5MF, ATP5MG, ATP5MPL, ATP5PB, ATP5PD, ATP5PF, ATP6AP1, ATP6AP2, ATP6V0A1, ATP6V0A2, ATP6V0D1, ATP6V0E1, ATP6V0E2, ATP6V1A, ATP6V1B2, ATP6V1C1, ATP6V1D, ATP6V1E1, ATP6V1F, ATP8B1, ATP8B2, ATPSCKMT, ATRX, ATXN10, ATXN7L2, ATXN7L3B, AURKA, AURKB, AUTS2, AVIL, AVPR2, AXIN1, AXIN2, AZI2, AZIN1, AZIN2, B2M, B3GAT1, B3GLCT, B4GALNT4, B4GAT1, B9D2, BACE1, BACH1, BACH2, BAG5, BAHCC1, BAHD1, BAK1, BAMBI, BASP1, BATF2, BAX, BBX, BCAS2, BCAT1, BCKDHA, BCKDHB, BCKDK, BCL11B, BCL2A1, BCL2L13, BCL7C, BCL9L, BCR, BDP1, BEGAIN, BEX2, BEX4, BEX5, BFAR, BFSP1, BHLHA15, BICDL1, BICRA, BIN1, BIN3, BIRC5, BLM, BLNK, BLOC1S4, BLVRA, BLVRB, BMERB1, BMF, BMI1, BMP2K, BMPR1A, BNC2, BNIP2, BNIP3, BOD1L1, BPI, BPTF, BRCA1, BRCA2, BRD1, BRD9, BRF2, BRI3, BRICD5, BRIX1, BRK1, BRPF3, BSG, BST1, BST2, BTBD2, BTBD3, BTBD9, BTF3L4, BTG1, BTG2, BTK, BTN3A1, BTN3A2, BTNL8, BUB1, BUB1B, BUB3, BZW2, C11orf24, C11orf65, C12orf29, C12orf4, C12orf57, C12orf75, C13orf46, C14orf119, C14orf132, C14orf28, C15orf41, C16orf54, C16orf70, C16orf91, C17orf107, C17orf58, C17orf67, C19orf12, C19orf25, C19orfi8, C19orf54, C19orf71, C19orf84, C1GALT1C1, C1orf115, C1orf162, C1orf21, C1orf216, C1orf35, C1orf43, C1orf50, C1QA, C1QB, C1QC, C2, C20orf194, C20orf204, C20orf27, C20orf96, C21orf91, C22orf19, C2CD5, C2orf49, C3AR1, C4orf50, C5, C5orf15, C5orf22, C5orf24, C5orf30, C6orf136, C7orf26, C8orf58, C9orf139, C9orf64, C9orf78, CA11, CA2, CA5B, CA8, CABIN1, CABP4, CACNA1H, CACNA1I, CACNA2D2, CACNA2D4, CACNB1, CACNB2, CACNG8, CACTIN, CALCOCO2, CALCRL, CALM2, CALU, CAMK1, CAMK1D, CAMK2G, CAMK2N1, CAMK4, CAMP, CAP1, CAPG, CAPN1, CAPN10, CAPN15, CAPN2, CAPN3, CAPNS1, CAPRIN1, CAPRIN2, CAPZA1, CAPZA2, CARD11, CARD16, CARD6, CARMIL2, CARNMT1, CARNS1, CASD1, CASP1, CASP7, CASP8, CASP8AP2, CASS4, CAST, CASTOR3, CAT, CATSPER1, CATSPER2, CATSPERB, CATSPERG, CBFA2T2, CBLB, CBR1, CBR4, CBWD1, CBWD2, CBWD3, CBWD5, CBWD6, CBX4, CBX7, CC2D1B, CCDC102A, CCDC12, CCDC120, CCDC136, CCDC138, CCDC141, CCDC146, CCDC149, CCDC157, CCDC159, CCDC17, CCDC18, CCDC191, CCDC200, CCDC28A, CCDC43, CCDC47, CCDC57, CCDC59, CCDC6, CCDC65, CCDC66, CCDC69, CCDC7, CCDC78, CCDC80, CCDC84, CCDC88A, CCDC88B, CCDC88C, CCDC91, CCDC92, CCL28, CCL3L1, CCL4, CCL4L2, CCL5, CCM2, CCN3, CCNA2, CCNB1, CCNB2, CCND2, CCNJ, CCNL2, CCNT1, CCNYL1, CCR1, CCR2, CCR3, CCR7, CCR9, CCRL2, CCSAP, CCSER2, CCT5, CCT6A, CCT8, CCZ1, CCZ1B, CD101, CD109, CD14, CD151, CD160, CD163, CD163L1, CD164, CD180, CD1A, CD1D, CD2, CD200R1, CD209, CD226, CD244, CD247, CD28, CD2BP2, CD300C, CD300LB, CD302, CD320, CD33, CD36, CD38, CD3D, CD3E, CD3G, CD40LG, CD47, CD5, CD6, CD63, CD69, CD7, CD81, CD86, CD93, CD96, CD99L2, CDAN1, CDC14A, CDC20, CDC25A, CDC25B, CDC37L1, CDC40, CDC42BPA, CDC42BPB, CDC42BPG, CDC42EP1, CDC42EP3, CDC42SE1, CDC42SE2, CDC45, CDC6, CDCA3, CDCA5, CDCA8, CDH24, CDHR1, CDHR3, CDIP1, CDK1, CDK11B, CDK13, CDK17, CDK20, CDK2AP2, CDK5, CDK5RAP2, CDK9, CDKN1B, CDKN1C, CDKN2AIP, CDKN2B, CDKN2C, CDT1, CEACAM1, CEACAM3, CEBPA, CEBPD, CENPF, CENPN, CENPT, CENPU, CENPV, CEP104, CEP120, CEP126, CEP131, CEP135, CEP152, CEP164, CEP170, CEP250, CEP290, CEP55, CEP68, CEP70, CEP78, CEP85L, CERCAM, CERK, CERS4, CERS6, CES1, CES1P1, CFAP20, CFAP298, CFAP36, CFAP410, CFAP44, CFAP45, CFH, CFP, CH25H, CHCHD1, CHCHD4, CHCHD6, CHD2, CHD3, CHD6, CHD7, CHERP, CHI3L1, CHIC1, CHID1, CHKA, CHML, CHMP2B, CHMP4A, CHP1, CHRFAM7A, CHRNA2, CHRNA7, CHRNE, CHST10, CHST12, CHST13, CHST2, CHST7, CHST8, CHTF18, CHTF8, CIAO2A, CIC, CINP, CIP2A, CIRBP, CISD1, CISH, CIT, CKAP5, CKB, CKS2, CLASRP, CLC, CLCF1, CLCN3, CLCN4, CLCN5, CLCN6, CLCN7, CLDN15, CLDND2, CLEC12A, CLEC12B, CLEC18A, CLEC18B, CLEC1B, CLEC2B, CLEC2D, CLEC4C, CLEC4D, CLEC40, CLEC5A, CLEC6A, CLEC9A, CLHC1, CLIC1, CLIC3, CLIC4, CLIC5, CLK1, CLN5, CLN6, CLN8, CLNS1A, CLPB, CLPTM1, CLPTM1L, CLSPN, CLSTN1, CLSTN3, CLTA, CLTC, CLTCL1, CMAS, CMC1, CMC2, CMKLR1, CMPK1, CMPK2, CMTM2, CMTM4, CMTM7, CNDP2, CNIH3, CNIH4, CNNM3, CNOT6L, CNP, CNPY4, CNTLN, CNTNAP1, CNTNAP2, COA3, COA4, COA5, COA7, COASY, COG8, COL13A1, COL18A1, COL6A1, COL6A2, COL8A2, COLGALT1, COLGALT2, COLQ, COMMD1, COMMD10, COMMD9, COMT, COPA, COPB2, COPG1, COPG2, COPS2, COPS3, COPZ1, COQ10A, COQ2, COQ5, CORO1C, CORO2B, CORO6, CORO7, COTL1, COX10, COX15, COX5A, COX5B, COX6A1, COX6B1, COX7A2L, COX7B, COX8A, CPA3, CPEB3, CPEB4, CPED1, CPM, CPNE2, CPNE8, CPSF1, CPSF2, CPSF3, CPVL, CRACR2A, CRAT, CREB1, CREBRF, CREBZF, CREG1, CRELD1, CREM, CRIM1, CRIP1, CRIP2, CRISPLD2, CRLF3, CRLS1, CROCC, CROCC2, CROT, CRTAP, CRTC2, CRY1, CRYBG1, CRYBG2, CRYBG3, CRYM, CS, CSF1, CSF1R, CSF2RA, CSGALNACT2, CSNK1A1, CSNK1E, CSNK1G2, CSNK2A1, CSNK2A3, CSPP1, CSRNP1, CST3, CST7, CSTA, CSTB, CTAGE15, CTAGE4, CTAGE6, CTAGE8, CTBP1-AS, CTC1, CTDSPL2, CTIF, CTNNA1, CTNNB1, CTNND1, CTNS, CTSA, CTSB, CTSC, CTSD, CTSF, CTSH, CTSL, CTSO, CTSS, CTSW, CTSZ, CTTNBP2NL, CUBN, CUEDC2, CUL1, CUX1, CWC15, CWF19L2, CXCL1, CXCL10, CXCL5, CXCL8, CXCR1, CXCR2, CXorf21, CXorf38, CYB561D1, CYB561D2, CYB5R1, CYB5R3, CYBB, CYBRD1, CYC1, CYCS, CYFIP1, CYFIP2, CYHR1, CYLD, CYP19A1, CYP1B1, CYP2D6, CYP2D7, CYP4F12, CYSLTR2, CYTH1, CYTH2, DAAM2, DAB2, DAD1, DAGLA, DALRD3, DAP, DAPK2, DARS2, DBF4, DBH, DBI, DBN1, DBP, DCAF15, DCAF16, DCLRE1A, DCPS, DCTN2, DCTN4, DCTN5, DCTN6, DDB1, DDHD2, DDI2, DDIT4, DDOST, DDX17, DDX21, DDX41, DDX49, DDX5, DDX6, DECR1, DEDD2, DEF6, DEFA1, DEFA1B, DEFA3, DENND10, DENND11, DENND1A, DENND1C, DENND2D, DENND5B, DEPP1, DERA, DERL3, DESI1, DGKE, DGKG, DGKK, DGKQ, DGKZ, DGUOK, DHCR24, DHFR, DHRS11, DHRS13, DHRS3, DHRS4, DHRS4L2, DHX29, DHX32, DHX33, DHX57, DHX9, DIAPH2, DIDO1, DIMT1, DIP2C, DLC1, DLD, DLEC1, DLEU7, DLG3, DLG4, DLG5, DLGAP5, DMAC2, DMAP1, DMPK, DMWD, DMXL1, DNAAF2, DNAH10, DNAH8, DNAJA1, DNAJA2, DNAJB1, DNAJB12, DNAJB13, DNAJB14, DNAJB9, DNAJC13, DNAJC15, DNAJC24, DNAJC5, DNAJC6, DNAL1, DNASE1, DNASE1L1, DNASE2, DNM1L, DNMT3A, DOCK1, DOCK2, DOCK7, DOCK8, DOCK9, DOK1, DOK4, DOK6, DOLPP1, DOP1B, DPAGT1, DPEP2, DPEP3, DPP3, DPP9-AS1, DPYD, DPYSL2, DRAM1, DRAM2, DRAXIN, DSE, DSTN, DTHD1, DTL, DTWD1, DTWD2, DTX3, DTX3L, DUOX1, DUS3L, DUSP16, DUSP2, DUSP3, DUSP7, DUSP8, DVL1, DVL2, DXO, DYM, DYNLL1, DYNLL2, DYNLT3, DYRK1A, DYRK1B, DYRK2, DYRK3, DYSF, DZIP3, E2F1, E2F2, E2F3, E2F4, E2F6, E4F1, EAF1, EAF2, EBF4, EBLN2, ECH1, ECHDC1, ECHDC2, ECHDC3, ECPAS, EDAR, EDEM2, EDEM3, EDNRB, EED, EEF1AKNMT, EFHC2, EFHD2, EFNA5, EFTUD2, EGFL7, EGLN1, EGR3, EHD4, EID3, EIF1, EIF1AD, EIF1AX, EIF2AK1, EIF2AK4, EIF2B1, EIF2B2, EIF2S1, EIF2S3, EIF2S3B, EIF3I, EIF3M, EIF4E2, EIF4EBP1, EIF4G1, EIF4H, EIF5A2, EIF5AL1, EIF6, ELAVL1, ELK4, ELL2, ELMO2, ELMO3, ELOB, ELOC, ELOVL1, ELP2, EMC7, EMC8, EMID1, EMILIN2, EML3, EML4, EMP3, ENKUR, ENO1, ENO2, ENO3, ENOX2, ENPP3, ENPP5, ENY2, EOMES, EPB41L3, EPB41L4A, EPC1, EPDR1, EPHA4, EPHB1, EPHB2, EPHB4, EPHX2, EPN2, EPPK1, EPS8, EPS8L2, EPSTI1, ERAL1, ERBB2, ERCC6L2, ERCC8, EREG, ERFL, ERG28, ERH, ERI2, ERLIN1, ERLIN2, ERMAP, ERN1, ERO1A, ERO1B, ERP27, ERP44, ESCO1, ESD, ESF1, ESPL1, ESR1, ESR2, ESRP2, ESYT2, ETAA1, ETF1, ETFA, ETFDH, ETHE1, ETS1, ETS2, EVI2A, EVI2B, EVI5, EVL, EWSR1, EXD3, EXOC4, EXOC6, EXOC8, EXOSC1, EXOSC4, EXOSC6, EXPH5, EXT1, EXT2, EZH2, F2RL2, F5, FABP5, FADS1, FAH, FAIM, FAM102A, FAM107B, FAM118B, FAM122B, FAM131B, FAM151B, FAM153B, FAM156A, FAM156B, FAM160B2, FAM169A, FAM172A, FAM174A, FAM177A1, FAM193B, FAM199X, FAM200B, FAM20A, FAM20C, FAM214A, FAM229A, FAM241A, FAM32A, FAM43A, FAM72A, FAM72B, FAM72C, FAM72D, FAM76A, FAM76B, FAM83A, FAM89A, FAM98C, FANCA, FANCI, FAT2, FAT4, FAXDC2, FBF1, FBL, FBLN7, FBN2, FBP1, FBRSL1, FBXL13, FBXL14, FBXL15, FBXL16, FBXL17, FBXL5, FBXL8, FBX03, FBXO31, FBXO32, FBXO33, FBXO45, FBXO5, FBXO6, FCER1A, FCGR1A, FCGR1B, FCGR3A, FCGR3B, FCGRT, FCHO1, FCHSD1, FCMR, FCN1, FCN2, FCRL3, FCRL5, FCRL6, FEN1, FERMT3, FES, FEZ1, FEZ2, FFAR2, FGD1, FGD2, FGD3, FGD4, FGD6, FGFBP2, FGFR1OP, FGFRL1, FGR, FH, FHDC1, FHL1, FIBP, FIG4, FIS1, FKBP15, FKBP1A, FKBP1B, FKBP5, FKBP9, FLT1, FLT3, FLVCR2, FLYWCH1, FMN1, FMNL3, FMO5, FN1, FNBP1L, FNDC9, FNIP2, FOSB, FOXD2-AS1, FOXK1, FOXM1, FOXN2, FOXO1, FOXP1, FOXP3, FOXP4, FPGT, FPR3, FRMD3, FRMD4B, FRMD8, FRMPD3, FRRS1, FSCN1, FSTL3, FTL, FUCA2, FURIN, FUT11, FXYD6, FYB1, FYN, FZD1, FZD2, FZD3, FZD5, FZD7, GOS2, G2E3, G6PC3, G6PD, GAA, GABRR2, GADD45B, GAL3ST4, GALK1, GALK2, GALNT11, GALNT12, GALNT2, GALNT3, GALNT7, GAN, GANC, GAPDH, GARS1, GART, GAS2L3, GAS6, GASK1B, GATA2, GATA3, GATAD2A, GATAD2B, GATB, GBA, GBE1, GBGT1, GCAT, GCC1, GCC2, GCNT1, GCNT4, GCSAM, GCSAML, GDAP1, GDE1, GDF11, GDI2, GDPD3, GEMIN7, GEN1, GET3, GFI1, GFM1, GFM2, GFRA2, GGACT, GGCT, GGH, GGT7, GHITM, GHRL, GIGYF1, GIMAP5, GIMAP7, GIMAP8, GINS2, GIPC1, GIPR, GK5, GKAP1, GLB1, GLB1L2, GLCCI1, GLCE, GLDC, GLDN, GLE1, GLI1, GLI4, GLIPR1, GLMP, GLO1, GLRX, GLRX3, GLS, GLTP, GLUD1, GLUD2, GM2A, GMCL1, GMDS, GMPPA, GMPR, GNA15, GNAL, GNAO1, GNB5, GNG2, GNG5, GNL2, GNLY, GNPAT, GNPDA1, GNPTAB, GNRH1, GNS, GOLGA4, GOLGA5, GOLGA6L10, GOLGA6L3, GOLGA6L4, GOLGA6L9, GOLGA7B, GOLGA8A, GOLGA8B, GOLT1B, GORASP1, GOSR1, GOT2, GPA33, GPALPP1, GPAT2, GPBAR1, GPD2, GPER1, GPI, GPM6B, GPN3, GPNMB, GPR146, GPR153, GPR155, GPR171, GPR174, GPR18, GPR183, GPR3, GPR34, GPR68, GPR75, GPRC5D, GPSM3, GPT2, GPX1, GPX4, GRAMD1C, GRB10, GRB2, GRHPR, GRIN3B, GRINA, GRK2, GRK3, GRK5, GRM2, GRN, GSR, GSTM1, GSTM2, GSTM4, GSTO1, GSTZ1, GTF2B, GTF2F2, GTF2H1, GTF3C6, GTPBP4, GTPBP8, GTSE1, GTSF1, GUF1, GUSB, GXYLT1, GYG1, GYPE, GYS1, GZMA, GZMB, GZMH, GZMK, GZMM, H1-0, H1-10, H1-4, H2AJ, H2AZ2, H2BC17, H2BC5, H3-3B, H4-16, H4C8, HAAO, HABP4, HADHA, HADHB, HAGHL, HAT1, HAUS1, HAUS4, HAUS5, HAVCR2, HCAR2, HCAR3, HCCS, HCN2, HCN3, HDAC8, HDAC9, HDC, HDGF, HDHD5, HDLBP, HEATR4, HEATR9, HEBP1, HECTD2, HEG1, HELB, HERC1, HES4, HEXB, HEXD, HFE, HGF, HIBADH, HIGD1A, HIGD2A, HINT2, HIP1R, HIRIP3, HIVEP2, HJURP, HK1, HK2, HK3, HKDC1, HLA-DQA2, HLA-DRA, HLA-E, HLA-F, HLX, HM13, HMBS, HMCES, HMGB2, HMGB3, HMGCL, HMGXB4, HMOX1, HMOX2, HNMT, HNRNPA0, HNRNPAB, HNRNPDL, HNRNPF, HNRNPK, HOMEZ, HOPX, HOXB2, HOXB3, HOXB4, HP, HPCAL1, HPCAL4, HPR, HPRT1, HPS5, HPSE, HRH4, HS1BP3, HS3ST3B1, HSBP1, HSD17B10, HSD17B12, HSD17B4, HSF2, HSF4, HSPA4, HSPH1, HTRA1, HUS1, HVCN1, HYAL2, IAH1, IBTK, ICA1, ID2, ID3, IDE, IDH1, IDH2, IDH3G, IDS, IER2, IER5, IFH6, IFI27L1, IFI27L2, IFI35, IFI44, IFI6, IFIT5, IFITM3, IFNAR1, IFNG, IFNGR1, IFNGR2, IFT122, IFT80, IGF1R, IGF2BP3, IGFBP2, IGFBP3, IGFBP7, IGIP, IGLL5, IK, IKBKE, IKZF1, IKZF2, IKZF3, IKZF4, IL11RA, IL12RB1, IL15, IL15RA, IL17RA, IL18, IL18BP, IL1B, IL1R2, IL21R, IL24, IL2RA, IL2RB, IL2RG, IL32, IL3RA, IL5RA, IL7R, IMMT, IMPA2, IMPACT, IMPAD1, ING5, INIP, INKA1, INO80C, INO80E, INPP1, INPP4A, INPP4B, INPP5D, INPP5E, INPPL1, INSR, INTS6, IP6K2, IPO7, IPP, IQCN, IQSEC3, IRAK1, IRAK1BP1, IRAK2, IRAK3, IRF2BP1, IRF3, IRF5, IRF8, ISG20L2, ISYNA1, ITFG1, ITGA1, ITGA7, ITGAM, ITGB2, ITGB7, ITGB8, ITK, ITM2A, ITM2C, ITPKB, ITPKC, ITPR3, ITPRID2, ITPRIPL1, ITPRIPL2, ITSN1, JADE1, JADE2, JADE3, JAG1, JAGN1, JAK1, JAK2, JAKMIP1, JAKMIP2, JAM3, JCHAIN, JDP2, JKAMP, JMY, JPH4, JUN, JUNB, JUND, JUP, KANK2, KANK3, KANSL1, KANSL2, KARS1, KAT6A, KAT6B, KATNBL1, KBTBD11, KBTBD4, KBTBD6, KCNA3, KCNC4, KCND3, KCNE1, KCNE1B, KCNE3, KCNK13, KCNMA1, KCNMB1, KCNQ1, KCTD12, KCTD13, KCTD3, KCTD5, KDELR1, KDELR2, KDM1B, KDM2A, KDM3A, KDM5A, KDM6B, KEL, KIAA0100, KIAA0355, KIAA0586, KIAA0895L, KIAA0930, KIAA1143, KIAA1257, KIAA1324, KIAA1328, KIAA1522, KIAA1671, KIAA1958, KIAA2026, KIF11, KIF14, KIF15, KIF18A, KIF18B, KIF19, KIF20B, KIF21A, KIF21B, KIF22, KIF23, KIF26A, KIF2A, KIF2C, KIF3A, KIF4A, KIF5C, KIFC1, KIFC2, KIFC3, KIR2DL1, KIR2DL3, KIR2DS4, KIR3DL1, KIR3DL2, KIZ, KLC2, KLC4, KLF12, KLF16, KLF2, KLF5, KLHDC2, KLHDC4, KLHDC8A, KLHL11, KLHL12, KLHL14, KLHL15, KLHL25, KLHL28, KLHL3, KLHL42, KLHL8, KLRB1, KLRC1, KLRC4, KLRD1, KLRF1, KLRG1, KMO, KMT2A, KMT2B, KMT2E, KMT5C, KNL1, KNSTRN, KPNA5, KPTN, KRBA1, KRI1, KRR1, KRT23, KRT72, KRT73, KRTCAP3, KY, L3MBTL3, LACC1, LACTB, LAIR1, LAMA2, LAMB2, LAMC1, LAMTOR2, LAMTOR4, LAMTOR5, LAP3, LAPTM4B, LAT, LAT2, LAX1, LBH, LCK, LCNL1, LCORL, LCP1, LDB1, LDHA, LDLR, LDLRAD3, LDOC1, LEMD3, LENG1, LENG8, LEPROT, LGALS1, LGALS12, LGALS3, LGALS8, LGALS9, LGALS9B, LGR6, LHFPL2, LHFPL6, LIG1, LIG4, LILRA4, LILRA5, LILRA6, LILRB4, LILRB5, LIM2, LIMD2, LIN54, LIN7C, LINC01410, LINC01579, LINGO1, LIPA, LIPE, LITAF, LIXIL, LLGL1, LLGL2, LMAN2, LMBR1, LMBRIL, LMF1, LMF2, LMNA, LMNB1, LMO2, LMO7, LMTK3, LNPEP, LONP2, LONRF3, LOXHD1, LOXL2, LPCAT1, LPCAT3, LPCAT4, LPL, LPXN, LRATD2, LRFN1, LRFN3, LRIF1, LRIG1, LRMDA, LRP1, LRP2BP, LRP3, LRP8, LRPAP1, LRRC14, LRRC23, LRRC37B, LRRC41, LRRC45, LRRC56, LRRC59, LRRC8D, LRRK1, LRWD1, LSM10, LSM6, LSS, LTA4H, LTB, LTBP3, LTBP4, LTBR, LTF, LUC7L, LUC7L3, LY6G5C, LY75, LY86, LY9, LYRM7, LYSMD4, LYZ, LZTFL1, LZTS3, M1AP, M6PR, MACROH2A1, MACROH2A2, MAEA, MAF, MAFB, MAFG, MAGED2, MAGEE1, MAGEF1, MALAT1, MAML3, MAN1A2, MAN1B1, MAN1C1, MAN2A2, MAN2B1, MANBA, MAOA, MAOB, MAP10, MAP11, MAP1LC3A, MAP2K1, MAP2K6, MAP3K10, MAP3K12, MAP3K20, MAP3K21, MAP3K6, MAP3K7CL, MAP3K9, MAP4K1, MAP4K2, MAP9, MAPK13, MAPK14, MAPK3, MAPK6, MAPK8, MAPKAPK3, MAPKBP1, MAPRE1, MAPRE2, MARC1, MARCHF1, MARCHF2, MARCHF5, MARCHF9, MARCKSL1, MARCO, MARS2, MARVELD1, MASP2, MAST3, MAT2A, MATK, MATR3, MBD5, MBLAC2, MBOAT1, MBP, MBTPS2, MC1R, MCEMP1, MCF2L, MCF2L2, MCFD2, MCM10, MCM2, MCM3AP-AS1, MCM4, MCMBP, MCOLN1, MCR1P1, MCTP1, MCTS1, MDGA1, MDH1, MDH2, MDS2, ME1, ME2, MECP2, MED1, MED10, MED15, MED17, MED19, MED20, MED21, MED30, MED31, MED6, MED8, MEF2A, MEF2C, MEGF6, MELK, MELTF, MERTK, MESD, METRN, METTL14, METTL22, METTL4, METTL7A, METTL9, MEX3C, MFGE8, MFSD1, MFSD14B, MFSD2B, MFSD8, MGAT1, MGAT4A, MGME1, MGST1, MGST2, MGST3, MIB2, MICA, MICAL2, MICB, MICU1, MID2, MIEF2, MIGA1, MIGA2, MILR1, MINDY2, MINK1, MIOS, MIR23A, MIS18BP1, MITF, MKI67, MKKS, MLANA, MLC1, MLEC, MLF1, MLKL, MLLT11, MLLT3, MLLT6, MLX, MLXIP, MME, MMP14, MMP17, MMP19, MMP23B, MMP24, MMP28, MOAP1, MOB1B, MOB3C, MORC4, MORN3, MPC1, MPDU1, MPEG1, MPHOSPH10, MPHOSPH8, MPND, MPP1, MPP6, MPRIP, MPV17, MPV17L2, MPZL3, MR1, MRC1, MRI1, MRM2, MROH6, MRPL10, MRPL12, MRPL13, MRPL15, MRPL16, MRPL18, MRPL19, MRPL23, MRPL28, MRPL3, MRPL33, MRPL36, MRPL37, MRPL41, MRPL47, MRPL51, MRPL55, MRPL57, MRPL58, MRPL9, MRPS10, MRPS15, MRPS16, MRPS18A, MRPS2, MRPS23, MRPS5, MRPS6, MRPS7, MRRF, MRTFB, MS4A2, MS4A3, MS4A4A, MS4A4E, MS4A6A, MSANTD2, MSANTD3, MSANTD4, MSH3, MSL1, MSR1, MSRB2, MT1E, MT1F, MT1X, MT2A, MT-ATP6, MTCH2, MTERF2, MTF1, MTFR1, MTHFD1, MTHFD2, MTHFR, MTI F3, MTMR10, MTMR14, MTMR6, MT-ND1, MT-ND2, MT-ND5, MT-ND6, MTPAP, MTR, MTX3, MUC12, MUC16, MUC6, MUTYH, MVD, MVK, MX1, MXD3, MYBL1, MYBL2, MYCBP, MYCT1, MYD88, MYDGF, MYEF2, MYH10, MYH11, MYH7B, MYL5, MYLIP, MYO10, MYO1E, MY06, MYO7A, MYO9A, MYOF, MYPOP, MYZAP, MZB1, MZT1, N4BP2L2, NAA20, NAA30, NAA80, NAALAD2, NACA2, NACC2, NAE1, NAGA, NAGK, NAGLU, NAIP, NANS, NAP1L1, NAP1L2, NAP1L3, NAP1L5, NAPA, NAT8B, NATD1, NAV1, NBEA, NBL1, NBPF3, NBR1, NCALD, NCAM1, NCAPG, NCAPH, NCAPH2, NCBP2AS2, NCEH1, NCF2, NCK2, NCKAP1L, NCOA3, NCR1, NCR3, NCR3LG1, NCSTN, NDRG2, NDUFA1, NDUFA11, NDUFA12, NDUFA2, NDUFA3, NDUFA4, NDUFA6, NDUFA8, NDUFA9, NDUFAB1, NDUFAF1, NDUFAF3, NDUFB1, NDUFB10, NDUFB3, NDUFB4, NDUFB5, NDUFB9, NDUFC1, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS5, NDUFS6, NDUFS7, NDUFV3, NECTIN1, NECTIN2, NEDD4, NEIL1, NEK3, NEK4, NEK6, NEK7, NELL2, NEMF, NEO1, NET1, NETO2, NEURL1, NFATC2, NFATC3, NFE2L3, NFE4, NFIA, NFIL3, NFS1, NHP2, NHSL1, NIBAN2, NINL, NIP7, NIPA1, NIPA2, NIPAL2, NIPAL3, NIPSNAP2, NIPSNAP3A, NKD1, NKG7, NKIRAS2, NLGN2, NLGN3, NLN, NLRC3, NLRC4, NLRP12, NLRP3, NLRP6, NME1, NME2, NMNAT1, NMT2, NMUR1, NOCT, NOG, NOL10, NOL12, NOL3, NOL4L, NOP10, NOP53, NOSIP, NOTCH1, NOTCH4, NOXA1, NPAT, NPC2, NPL, NPR2, NPRL2, NPTXR, NR3C2, NREP, NRF1, NRG1, NRIP1, NRM, NRROS, NSDHL, NSG1, NSMCE3, NSMF, NSUN2, NT5DC2, NT5DC3, NTRK1, NTSR1, NUAK1, NUBP1, NUBP2, NUCB1, NUDT16, NUDT6, NUMA1, NUMBL, NUP37, NUP43, NUP58, NUP93, NUSAP1, NUTF2, NUTM2F, NUTM2G, OAF, OAS1, OAS2, OAS3, OASL, OBSCN, OCIAD2, OCLN, OCRL, ODF2L, OFD1, OGDH, OGFR, OLAH, OLFML2A, OLIG1, OPA1, OPLAH, OPN3, OR2A4, OR2A7, OR2B6, ORAI1, ORAI2, ORAI3, ORC1, ORC2, ORC5, ORMDL2, ORMDL3, OS9, OSBPL11, OSBPL5, OSBPL7, OSM, OSTC, OTOF, OTUD3, OTUD7B, OTULINL, OXA1L, OXR1, P2RX4, P2RX7, P2RY1, P2RY10, P2RY14, P2RY8, P3H4, P4HA1, P4HB, PABPC3, PACC1, PACS1, PACSIN1, PADI2, PAFAH2, PAIP2B, PAK1IP1, PALLD, PANX1, PAPOLG, PAPSS1, PAQR4, PARD6B, PARP10, PARP15, PARP16, PARP4, PARVG, PASK, PATJ, PATL2, PAX8, PAXX, PBX4, PBXIP1, PCCB, PCDH9, PCED1A, PCF11, PCK2, PCMT1, PCNA, PCNX2, PCNX3, PCOLCE, PCSK7, PCSK9, PCTP, PCYT2, PDCD10, PDCD4, PDCD6IP, PDCD7, PDE12, PDE1B, PDE2A, PDE3B, PDE7A, PDGFC, PDGFD, PDHB, PDIA3, PDIA5, PDIA6, PDK2, PDK4, PDP2, PDRG1, PDSS1, PDXK, PDZD2, PDZD4, PELP1, PEPD, PER1, PER3, PET100, PEX1, PEX11G, PFDN6, PFKFB3, PFN2, PGA3, PGAM1, PGAM4, PGAP3, PGBD2, PGD, PGGHG, PGK1, PGLS, PGLYRP1, PGM2, PGM2L1, PHAX, PHC1, PHETA2, PHF1, PHF10, PHF13, PHF19, PHF20, PHKB, PHLDB2, PHLDB3, PHLPP2, PHRF1, PI16, PI3, PICK1, PIGF, PIGL, PIGN, PIGS, PIK3C2B, PIK3CB, PIK3CD, PILRB, PIM1, PIN1, PINK1, PIP5K1B, PITPNC1, PITPNM1, PITPNM2, PITRM1, PIWIL4, PJA1, PJVK, PKIA, PKM, PKMYT1, PKN1, PKNOX1, PKP4, PLA2G12A, PLA2G15, PLA2G4A, PLA2G6, PLA2G7, PLAA, PLAAT3, PLAU, PLBD1, PLCB3, PLCD1, PLCD3, PLCH2, PLCL1, PLCXD2, PLD1, PLD3, PLD4, PLEKHA1, PLEKHA5, PLEKHB1, PLEKHB2, PLEKHF1, PLEKHG2, PLEKHG3, PLEKHG5, PLEKHH2, PLEKHM2, PLGLB1, PLIN2, PLIN3, PLK1, PLLP, PLOD1, PLP2, PLPBP, PLSCR1, PLXDC1, PLXDC2, PLXNA1, PLXNA3, PLXNA4, PMAIP1, PMEL, PMVK, PNISR, PNKD, PNKP, PNN, PNP, PNPO, PNRC1, PODN, PODXL, POFUT1, POFUT2, POLD3, POLDIP2, POLDIP3, POLE4, POLQ, POLR2D, POLR2E, POLR2G, POLR2M, POLR3G, POLRMT, POMP, PON2, POP7, POTEF, POTEI, POTEJ, POU2AF1, POU6F1, PPARD, PPARG, PPARGC1B, PPCDC, PPCS, PPFIA3, PPFIBP2, PPIA, PPIB, PPIG, PPL, PPM1K, PPM1N, PPOX, PPPICC, PPP1R12C, PPP1R13B, PPP1R15A, PPP1R16B, PPP1R2, PPP1R26, PPP1R35, PPP1R37, PPP1R3D, PPP1R8, PPP2CB, PPP2R2B, PPP2R2D, PPP2R3B, PPP2R5C, PPP3CC, PPP6C, PPT1, PRAF2, PRAG1, PRAM1, PRCP, PRDM1, PRDM11, PRDM8, PRDX1, PRDX3, PRDX4, PRDX5, PRDX6, PREB, PRELID1, PREP, PRF1, PRKAA1, PRKAB1, PRKACA, PRKACB, PRKAG1, PRKCH, PRKCQ, PRKCZ, PRKD2, PRKRIP1, PRMT2, PRMT5, PROSER1, PRPF38A, PRPF38B, PRPF39, PRPF4, PRPF40B, PRR11, PRR12, PRR14, PRR5, PRR5L, PRR7, PRRC2C, PRRG4, PRRT3, PRRT4, PRSS23, PRSS33, PRSS53, PRSS57, PSAP, PSD, PSD3, PSD4, PSEN1, PSEN2, PSIP1, PSMA4, PSMA5, PSMA6, PSMA7, PSMB1, PSMB2, PSMB3, PSMB5, PSMB6, PSMB7, PSMC1, PSMD1, PSMD10, PSMD11, PSMD14, PSMD2, PSMD3, PSMD4, PSMD5, PSMD8, PSMG1, PSMG2, PSPH, PSTK, PSTPIP2, PTBP1, PTBP2, PTCD1, PTCH1, PTDSS1, PTGDR, PTGDR2, PTGDS, PTGER2, PTGER4, PTGFRN, PTGS2, PTK7, PTOV1, PTP4A3, PTPA, PTPMT1, PTPN11, PTPN2, PTPN4, PTPN7, PTPN9, PTPRO, PTPRS, PTRHD1, PTS, PTTG1, PTTG1IP, PUDP, PUM2, PURA, PUS7L, PVR, PXK, PXN, PYCARD, PYGM, PYGO2, PYHIN1, PYM1, PZP, QRICH2, QSER1, QSOX1, QTRT2, R3HDM1, RAB10, RAB11FIP3, RAB11FIP4, RAB11FIP5, RAB13, RAB15, RAB20, RAB22A, RAB32, RAB34, RAB37, RAB39A, RAB39B, RAB43, RAB44, RAB6D, RAB7A, RAB8A, RABEP2, RABGAP1L, RABL2B, RAC1, RACGAP1, RAD1, RAD23B, RAD51AP1, RAD52, RAD9A, RADX, RALA, RALGDS, RAN, RANBP6, RAP2A, RAP2C, RAPGEF5, RAPGEF6, RAPH1, RARG, RASA2, RASA3, RASAL3, RASGEF1B, RASGRF2, RASGRP1, RASGRP2, RASSF1, RASSF2, RASSF5, RASSF7, RB1, RBBP6, RBBP8, RBKS, RBL2, RBM14, RBM14-RBM4, RBM25, RBM34, RBM4, RBM45, RBM48, RBMS2, RBP7, RBPMS, RBX1, RCAN1, RCAN3, RCBTB2, RCC1, RCC2, RCE1, RCN2, RDH13, RDH14, RDH5, RDX, RECK, REEP4, REEP6, REM2, RENBP, RESF1, REST, RETREG1, RETREG3, REX1BD, REXO1, RFC2, RFTN1, RFX1, RFXAP, RGL4, RGMB, RGPD5, RGPD6, RGS1, RGS14, RGS16, RGS3, RGS6, RGS9, RHAG, RHBDD1, RHBDF2, RHCE, RHEB, RHEBL1, RHO, RHOA, RHOBTB3, RHOC, RHOF, RHOQ, RHOT1, RHOT2, RHOU, RHPN1, RIC1, RIC8B, RILPL1, RILPL2, RIMS3, RIN1, RIN2, RINL, RIOK3, RIOX1, RMI1, RNASE1, RNASE2, RNASE3, RNASE6, RNF10, RNF103, RNF126, RNF130, RNF135, RNF139, RNF144A, RNF144B, RNF165, RNF167, RNF175, RNF181, RNF182, RNF216, RNF217, RNF41, RNF43, RNF44, RNF7, RNH1, RNPEP, ROGDI, ROMO1, RORA, RPE, RPF1, RPGR, RPH3A, RPL13A, RPL17, RPL22L1, RPL26L1, RPL3, RPN1, RPN2, RPRD2, RPS14, RPS27A, RPS27L, RPS29, RPS3, RPS5, RPS6KA5, RPS6KC1, RPTOR, RPUSD2, RRAGA, RRAS, RRAS2, RRM2, RRP15, RSAD1, RSAD2, RSBN1, RSBN1L, RSF1, RSPRY1, RSRP1, RTL6, RTL8C, RTN4, RTRAF, RTTN, RUFY3, RUFY4, RUNDC1, RUNX3, RUSC2, RXFP2, RXFP4, RXRA, RYK, RYR3, S100A10, S100A11, S100A12, S100A4, S100A6, S100A8, S100A9, S1PR1, S1PR3, S1PR4, S1PR5, SACMIL, SAFB2, SALL2, SAMD10, SAMD3, SAMHD1, SAMSN1, SAP30, SAP30L, SAPCD2, SAR1B, SARDH, SARM1, SASH1, SASS6, SAT2, SBDS, SBF1, SBF2, SBK1, SCAI, SCAMP2, SCAP, SCAPER, SCARB1, SCARB2, SCCPDH, SCD, SCD5, SCFD1, SCIMP, SCML4, SCNM1, SCP2, SCPEP1, SCR1B, SDC1, SDC3, SDC4, SDCBP, SDCCAG8, SDE2, SDHB, SDHC, SDHD, SDK2, SEC11A, SEC23B, SEC23IP, SEC24A, SEC24D, SEC31A, SEC61A1, SEC61A2, SEC61B, SEC61G, SELENOF, SELENOM, SELENON, SELL, SEMA4A, SEMA4C, SEMA4F, SEMA6A, SEMA6B, SEMA6C, SENP7, SEPHS2, SEPTIN1, SEPTIN10, SEPTIN2, SEPTIN4, SEPTIN6, SEPTIN7, SEPTIN8, SEPTIN9, SERF1A, SERF2, SERHL2, SERP1, SERPINB1, SERPINB10, SERPINB2, SERPINB8, SERPINB9, SERPINE1, SERPING1, SESTD1, SETBP1, SETD1A, SETD1B, SETD3, SETD6, SETD7, SEZ6L, SF1, SF3A2, SF3B3, SFH, SFMBT1, SFMBT2, SFSWAP, SFT2D1, SFXN4, SFXN5, SGCD, SGF29, SGIP1, SGK3, SGMS1, SGMS2, SGO1, SGPP1, SGSH, SGSM1, SH2B1, SH2D1B, SH2D2A, SH2D3A, SH2D3C, SH2D4A, SH3BGRL, SH3BGRL3, SH3BP1, SH3BP4, SH3PXD2B, SH3RF1, SH3TC1, SH3YL1, SHCBP1, SHISA7, SHISAL2A, SHLD2, SHMT1, SHMT2, SHROOM1, SHTN1, SIAE, SIAH2, SIDT1, SIGIRR, SIGLEC1, SIGLEC11, SIGLEC12, SIGLEC15, SIGLEC16, SIGLEC9, SIKE1, SIL1, SIN3A, SIPA1, SIRPA, SIRPB2, SIRPD, SIVA1, SKAP1, SKAP2, SKI, SKIV2L, SLAIN1, SLAMF1, SLAMF6, SLC11A1, SLC11A2, SLC12A2, SLC13A4, SLC16A1, SLC16A11, SLC16A5, SLC16A6, SLC16A8, SLC19A2, SLC1A3, SLC1A5, SLC1A7, SLC22A15, SLC22A16, SLC24A4, SLC25A11, SLC25A24, SLC25A26, SLC25A29, SLC25A30, SLC25A38, SLC25A40, SLC25A42, SLC25A43, SLC25A45, SLC25A5, SLC25A53, SLC25A6, SLC26A11, SLC26A6, SLC27A1, SLC27A3, SLC29A2, SLC29A3, SLC2A4, SLC2A4RG, SLC2A5, SLC2A9, SLC30A1, SLC30A4, SLC31A1, SLC31A2, SLC33A1, SLC35A1, SLC35A3, SLC35A5, SLC35B1, SLC35B3, SLC35D1, SLC35D2, SLC35E2B, SLC35F6, SLC36A1, SLC36A4, SLC37A2, SLC38A1, SLC38A2, SLC38A5, SLC38A7, SLC39A1, SLC39A11, SLC39A13, SLC39A7, SLC39A9, SLC3A2, SLC41A1, SLC43A1, SLC43A3, SLC44A1, SLC45A3, SLC45A4, SLC46A2, SLC49A3, SLC4A11, SLC4A2, SLC4A4, SLC4A5, SLC4A7, SLC50A1, SLC5A3, SLC6A12, SLC6A16, SLC7A7, SLC9A3R1, SLC9A9, SLC9B2, SLCO4A1, SLF1, SLFN11, SLFN12, SLFN12L, SLIRP, SLITRK4, SLPI, SMAD1, SMAD3, SMAD4, SMAD7, SMARCAL1, SMARCD3, SMCO4, SMG7, SMIM10L2A, SMIM12, SMIM15, SMIM24, SMIM27, SMIM3, SMIM4, SMPD3, SMS, SMTN, SMU1, SMURF2, SMYD3, SMYD4, SNAPIN, SND1, SNF8, SNPH, SNRK, SNRNP25, SNRNP48, SNRNP70, SNRPB2, SNRPC, SNRPD2, SNRPD3, SNRPG, SNTA1, SNTB1, SNUPN, SNURF, SNX1, SNX10, SNX12, SNX17, SNX19, SNX2, SNX25, SNX29, SNX3, SNX30, SNX33, SNX5, SNX8, SOAT1, SOCS2, SOCS6, SORBS3, SORD, SORL1, SORT1, SOWAHC, SOWAHD, SOX12, SOX13, SOX8, SP4, SPAG16, SPAG5, SPATA33, SPATA5, SPATS2, SPATS2L, SPCS1, SPCS2, SPDYE3, SPECC1, SPEF2, SPG21, SPG7, SPHK1, SPIDR, SPINDOC, SPINT1, SPINT2, SPN, SPNS3, SPOCK1, SPOCK2, SPON1, SPON2, SPOUT1, SPR, SPRN, SPRY2, SPRYD3, SPSB1, SPSB2, SPTAN1, SPTB, SPTBN5, SPTLC1, SPTLC2, SPTSSA, SQLE, SQOR, SRA1, SRD5A1, SRD5A3, SRGAP1, SRGAP2, SRGAP2B, SRGAP2C, SRGAP3, SRP54, SRP72, SRP9, SRPK2, SRPK3, SRPRA, SRRT, SRSF1, SRSF11, SRSF5, SRSF7, SSBP3, SSBP4, SSR1, SSR3, SSR4, ST14, ST3GAL3, ST3GAL4, ST6GAL1, ST6GALNAC3, ST6GALNAC4, ST8SIA1, ST8SIA6, STAB1, STAC3, STAG3L3, STARD13, STARD3NL, STARD8, STARD9, STAT1, STAT2, STAT4, STAT5B, STEAP3, STIL, STIM2, STING1, STK10, STK26, STK3, STK39, STMN3, STMP1, STON1, STS, STT3A, STT3B, STX10, STX12, STX4, STYXL1, SUCLA2, SUCLG1, SULT1A1, SULT1A2, SUMF1, SUMO3, SUN2, SUOX, SURF4, SUSD3, SV2A, SVIP, SWAP70, SYDE2, SYK, SYN2, SYNE1, SYNE2, SYNE3, SYNGAP1, SYNGR2, SYNJ2, SYNM, SYNRG, SYTL1, SYTL2, SYTL3, TAF10, TAF12, TAF3, TAF4, TAF7, TAF9, TAGAP, TAGLN2, TAL1, TALDO1, TANC2, TAOK2, TARS1, TARS3, TBC1D1, TBC1D10A, TBC1D10C, TBC1D13, TBC1D16, TBC1D17, TBC1D19, TBC1D2, TBC1D25, TBC1D31, TBC1D3B, TBC1D3D, TBC1D3F, TBC1D3H, TBC1D3I, TBC1D3L, TBC1D4, TBC1D5, TBC1D8, TBCC, TBKBP1, TBL2, TBX21, TBXAS1, TC2N, TCAF1, TCAF2, TCAIM, TCEA2, TCEA3, TCEAL4, TCF20, TCF7, TCN1, TCN2, TCOF1, TCP11L2, TCTEX1D4, TCTN2, TDRD9, TEC, TECR, TEDC1, TEF, TEFM, TENT4B, TESPA1, TET3, TEX2, TEX52, TFCP2, TFDP1, TFDP2, TFEC, TFG, TFRC, TGFB3, TGFBR1, TGFBR2, TGFBR3, TGM2, THAP1, THAP5, THAP7, THBS1, THBS4, THEM4, THG1L, THOC6, THOC7, THUMPD1, THUMPD2, THUMPD3, TIAM2, TIGAR, TIGD1, TIGD2, TIGD3, TIGD5, TIMM13, TIMM23, TIMM8B, TIMMDC1, TIMP1, TIMP2, TIMP4, TJP3, TK1, TK2, TKFC, TKT, TKTL1, TLE2, TLN2, TLR2, TLR4, TLR5, TM2D3, TM7SF3, TM9SF2, TM9SF4, TMA16, TMBIM6, TMC6, TMC8, TMCC2, TMCC3, TMCO1, TMED8, TMED9, TMEM106A, TMEM11, TMEM115, TMEM116, TMEM120B, TMEM121B, TMEM131, TMEM134, TMEM144, TMEM147, TMEM14A, TMEM14C, TMEM150B, TMEM161B, TMEM165, TMEM167A, TMEM170B, TMEM179B, TMEM181, TMEM184A, TMEM184B, TMEM185B, TMEM204, TMEM205, TMEM208, TMEM218, TMEM219, TMEM222, TMEM230, TMEM243, TMEM25, TMEM254, TMEM255A, TMEM255B, TMEM258, TMEM259, TMEM263, TMEM268, TMEM272, TMEM273, TMEM38A, TMEM39A, TMEM39B, TMEM41B, TMEM45A, TMEM45B, TMEM50B, TMEM60, TMEM62, TMEM63A, TMEM63C, TMEM64, TMEM65, TMEM67, TMEM69, TMEM70, TMEM8B, TMEM9B, TMIGD2, TMIGD3, TMLHE, TMSB15B, TMTC1, TMTC2, TMTC3, TMUB1, TMX1, TMX2, TNFAIP8L2, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFRSF17, TNFRSF18, TNFRSF25, TNFSF10, TNFSF13, TNFSF8, TNIK, TNNT3, TNRC6B, TNRC6C, TNS2, TNS3, TOB1, TOB2, TOE1, TOGARAM2, TOLLIP, TOM1L2, TOMM22, TOMM40L, TOP1MT, TOP2A, TOPORS, TOR1A, TOR3A, TOR4A, TOX, TOX4, TP53BP1, TP53BP2, TP53I13, TP53I3, TP53TG5, TPCN2, TPI1, TPK1, TPM2, TPM4, TPMT, TPP1, TPPP, TPPP3, TPRG1, TPRG1L, TPST1, TPX2, TRA2A, TRA2B, TRABD2A, TRADD, TRAF1, TRAF3IP3, TRAF4, TRAF7, TRAFD1, TRANK1, TRAP1, TRAPPC10, TRAPPC11, TRAPPC2, TRAPPC3, TRAPPC4, TRAPPC6A, TRAT1, TREM1, TREML2, TRERF1, TREX2, TRGC1, TRIM23, TRIM28, TRIM32, TRIM33, TRIM46, TRIM56, TRIM59, TRIM62, TRIM7, TRIM71, TRIM73, TRIP12, TRIP13, TRIQK, TRIR, TRMT10C, TRMT11, TRMT13, TRMT2B, TRMT6, TRPC1, TRPC6, TRPM2, TRPS1, TSC22D4, TSEN54, TSG101, TSHR, TSHZ1, TSHZ2, TSPAN13, TSPAN18, TSPAN2, TSPAN3, TSPAN32, TSPAN4, TSPO, TSPOAP1, TSPYL1, TSPYL2, TSPYL4, TSSK6, TSTA3, TSTD1, TTC14, TTC16, TTC17, TTC22, TTC3, TTC33, TTC38, TTC39B, TTC9, TTK, TTL, TTPAL, TUBA1A, TUBA1B, TUBB, TUBB2A, TUBE1, TUBG1, TUBGCP2, TUBGCP3, TUBGCP6, TUFM, TUT4, TVP23C, TWF2, TWSG1, TXLNG, TXN, TXN2, TXNDC11, TXNDC15, TXNDC17, TXNDC5, TXNL1, TXNL4B, TXNRD2, TYMP, TYMS, TYSND1, UACA, UAP1L1, UBA1, UBA3, UBAP1, UBAP1L, UBE2C, UBE2E1, UBE2E2, UBE2H, UBE2J1, UBE2K, UBE2L3, UBE2L6, UBE2S, UBE3D, UBL3, UBQLN1, UBQLN2, UBQLN4, UBTD1, UBTD2, UBTF, UBXN11, UBXN8, UCP3, UGCG, UGGT2, UNC119B, UNC13B, UNC50, UNC5CL, UNC93B1, UNK, UNKL, UPF3B, UPP1, UPRT, UQCR10, UQCR11, UQCRC1, UQCRC2, UQCRFS1, UQCRH, UQCRHL, UQCRQ, URI1, UROD, USP11, USP18, USP20, USP21, USP39, USP41, USP42, USP51, USP54, USP6NL, USP9Y, UST, UTP11, UTP23, UVRAG, UVSSA, VAMP1, VAMP2, VAMP3, VAMP4, VAMP5, VAMP7, VAMP8, VAPA, VARS1, VASH1, VCAN, VDAC1, VDAC2, VDR, VEGFB, VENTX, VIM, VIPAS39, VNN1, VPS11, VPS25, VPS26B, VPS26C, VPS35, VPS35L, VPS37A, VPS45, VPS54, VRK2, VSIG1, VSIG10L, VSIG4, VTA1, VTI1B, VXN, WARS2, WASF1, WASHC2A, WASHC2C, WASHC4, WASHC5, WASL, WDFY1, WDR12, WDR18, WDR27, WDR35, WDR41, WDR54, WDR60, WDR61, WDR62, WDSUB1, WFDC1, WHAMM, WHRN, WIPF1, WNT10B, WNT11, WNT7A, WSB1, WWC2, WWP1, XCL1, XCL2, XK, XKR6, XKR8, XPC, XPNPEP1, XPNPEP2, XPO6, XPO7, XRCC2, XRCC3, XRCC4, XRCC5, XRN2, XRRA1, XXYLT1, XYLT1, YAF2, YEATS2, YES1, YIF1A, YIF1B, YIPF1, YIPF2, YIPF6, YPEL1, YPEL2, YPEL4, YPEL5, YRDC, YWHAE, YWHAG, YWHAH, YY1, YY1AP1, ZAP70, ZBED2, ZBTB1, ZBTB10, ZBTB14, ZBTB16, ZBTB18, ZBTB20, ZBTB25, ZBTB32, ZBTB38, ZBTB4, ZBTB40, ZBTB43, ZBTB44, ZBTB46, ZBTB7A, ZC3H12B, ZC3H12C, ZC3H12D, ZC3H13, ZC3H6, ZC3H8, ZC3HAV1, ZCCHC14, ZCCHC18, ZCCHC2, ZCCHC3, ZDHHC11, ZDHHC11B, ZDHHC12, ZDHHC18, ZDHHC20, ZDHHC3, ZDHHC5, ZDHHC8, ZEB1, ZFAND5, ZFP1, ZFP14, ZFP30, ZFP41, ZFP57, ZFP62, ZFP82, ZFP91, ZFPM1, ZFYVE26, ZFYVE27, ZFYVE28, ZHX2, ZMAT5, ZMPSTE24, ZMYM1, ZMYM4, ZMYM5, ZMYND11, ZMYND19, ZNF100, ZNF106, ZNF107, ZNF12, ZNF121, ZNF131, ZNF136, ZNF138, ZNF148, ZNF160, ZNF169, ZNF175, ZNF182, ZNF200, ZNF213, ZNF236, ZNF248, ZNF250, ZNF251, ZNF26, ZNF260, ZNF264, ZNF266, ZNF274, ZNF276, ZNF286A, ZNF287, ZNF292, ZNF32, ZNF324, ZNF329, ZNF330, ZNF335, ZNF33B, ZNF345, ZNF350, ZNF365, ZNF366, ZNF382, ZNF383, ZNF394, ZNF414, ZNF428, ZNF429, ZNF430, ZNF439, ZNF44, ZNF441, ZNF446, ZNF461, ZNF469, ZNF48, ZNF483, ZNF486, ZNF487, ZNF506, ZNF507, ZNF517, ZNF519, ZNF529, ZNF540, ZNF548, ZNF549, ZNF552, ZNF562, ZNF566, ZNF567, ZNF568, ZNF569, ZNF570, ZNF573, ZNF574, ZNF575, ZNF577, ZNF579, ZNF587, ZNF599, ZNF600, ZNF608, ZNF611, ZNF622, ZNF644, ZNF652, ZNF665, ZNF674, ZNF680, ZNF688, ZNF697, ZNF699, ZNF703, ZNF707, ZNF71, ZNF720, ZNF736, ZNF737, ZNF74, ZNF770, ZNF782, ZNF783, ZNF789, ZNF793, ZNF80, ZNF827, ZNF83, ZNF830, ZNF831, ZNF836, ZNF850, ZNF853, ZNF862, ZNF865, ZNF91, ZNF92, ZNHIT6, ZNRD2, ZRANB2, ZSCAN18, ZSWIM5, ZSWIM6, ZSWIM9, ZW10, ZWINT, ZXDA, ZXDB Lung-CoV2 to Lung-CTL (2,220 DEGs in Lung) A2M, AAK1, ABCC3, ABCF1, ABB, ABLIM1, ABLIM3, ABR, ABT1, ABTB1, ACAD8, ACADVL, ACO2, ACOD1, ACOT1, ACP2, ACSL1, ACSS1, ACTB, ACTL6A, ACTN4, ACTR1B, ACVR1, ACVRL1, ADA2, ADAM15, ADAM17, ADAMDEC1, ADAMTS1, ADAMTS13, ADAMTS2, ADAMTS9, ADAMTSL3, ADAP1, ADCY4, ADCY6, ADCYAP1, ADD1, ADGRD1, ADGRE1, ADGRE5, ADGRG3, ADGRL2, ADH1B, ADIPOR2, ADNP2, ADRA2A, AEBP1, AEBP2, AEN, AFAP1L1, AFDN, AFF4, AFG3L2, AFMID, AGAP3, AGAP4, AGAP6, AGPAT2, AHNAK, AIF1L, AIM2, AIP, AKAP1, AKAP13, AKAP17A, AKNA, AKR1B10, AKR1B15, AKT3, ALAS1, ALDH3A1, ALDOC, ALKBH5, ALKBH6, ALOX5AP, ALPK1, ALPL, ALS2CL, AMBRA1, AMFR, AMOTL1, ANAPC11, ANGEL1, ANGPTL2, ANGPTL6, ANKDD1A, ANKRD10, ANKRD22, ANKRD54, ANKS1A, ANKZF1, ANO6, ANP32A, ANP32D, ANXA2R, ANXA6, AOC3, AP2A2, APBB1IP, APH1A, APOBEC3A, APOL6, AQP1, AQP9, ARAP3, ARC, ARF5, ARFGAP1, ARFRP1, ARHGAP10, ARHGAP4, ARHGAP9, ARHGDIB, ARHGEF15, ARHGEF25, ARHGEF7, ARL13B, ARL5B, ARMC5, ARMC6, ARPC5L, ARRB2, ARRDC2, ARSL, ASB1, ASB13, ASB6, ASB8, ASCL4, ASL, ASMTL, ASXL1, ASXL2, ATAD3A, ATAD3B, ATF4, ATF6B, ATG101, ATG16L1, ATG4B, ATP1A1, ATP1B4, ATP2A3, ATP5MF, ATP6V0A1, ATP6V0A2, ATP6V0D1, ATP7B, ATRX, ATXN7L3, AUP1, B4GALT2, B4GALT3, B4GALT7, BAALC, BAG3, BAG6, BAIAP2, BAIAP2L1, BANF1, BANP, BAP1, BASP1, BAZ2A, BBOF1, BBS1, BBS4, BCAR1, BCAT1, BCAT2, BCL2A1, BCL2L14, BCL2L2, BCL3, BCOR, BEST1, BHLHE40, BIN1, BIN2, BIN3, BLCAP, BLOC1S1, BMS1, BRD9, BSDC1, BST1, BTBD17, BTBD19, BTG2, BTN2A2, BTNL9, BUD13, BUD23, BYSL, C12orf10, C12orf57, C14orf132, C15orf48, C19orf84, C1orf194, C1orf216, C1QB, C1QC, C1QTNF1, C2, C20orf203, C20orf27, C2CD2, C3AR1, C3orf86, C4orB, C4orf50, C5AR1, C6, C6orf201, C6orf47, C7orf25, C7orf50, C8A, C8orB3, C8orf58, CA1, CA12, CA8, CAB39L, CACNA1A, CACNA1C, CACNA1E, CACNG6, CALHM2, CALR, CAMP, CANT1, CAP1, CAPRIN2, CAPZA1, CARD16, CARD17, CASP1, CASP4, CASP5, CAVIN1, CAVIN3, CBFA2T2, CBX4, CBX7, CCAR1, CCDC124, CCDC130, CCDC137, CCDC185, CCDC186, CCDC194, CCDC38, CCDC57, CCDC60, CCDC69, CCDC71L, CCDC84, CCDC86, CCDC9, CCL11, CCL15, CCL18, CCL19, CCL2, CCL3, CCL3L1, CCL4, CCL4L2, CCL7, CCL8, CCM2, CCN2, CCN5, CCND1, CCND3, CCNL2, CCPG1, CCR1, CCR7, CCRL2, CCT4, CCT5, CCT8, CD164, CD2BP2, CD320, CD34, CD37, CD38, CD4, CD53, CD55, CD69, CD74, CD82, CD8A, CD9, CDA, CDC37, CDC42BPB, CDCA7, CDH11, CDH2, CDH5, CDHR5, CDK10, CDK18, CDK4, CDK9, CDKN2AIP, CEACAM1, CEACAM3, CEACAM6, CEACAM8, CELA3B, CEMIP2, CENPC, CENPT, CEP68, CERK, CERS5, CERS6, CERT1, CETN1, CFAP20, CFAP300, CFAP36, CFAP77, CFL1, CFLAR, CGRRF1, CHD2, CHI3L1, CHI3L2, CHID1, CHIT1, CHMP1A, CHRAC1, CHROMR, CIB1, CIRI, CIRBP, CKB, CKS1B, CLC, CLCN6, CLDN2, CLDN4, CLDN5, CLEC12A, CLEC12B, CLEC1A, CLEC4A, CLEC4D, CLEC4E, CLEC7A, CLIC3, CLIP4, CLPS, CLPTM1L, CMC2, CMPK2, CMTM2, CNOT1, CNST, CNTN2, CNTROB, COASY, COG1, COG4, COL12A1, COL16A1, COL2A1, COL9A2, COLGALT1, COPZ2, CORO1C, COX4I1, CPA5, CPAMD8, CPE, CPLX2, CPSF7, CPXM2, CR1, CRABP1, CRAMP1, CRCT1, CREB3L2, CREBZF, CRELD2, CRIP2, CRISP3, CRTC2, CRY2, CRYAB, CSF2RB, CSF3R, CSNK1A1, CSNK1D, CSNK2A2, CSNK2B, CSPG4, CSRNP1, CST7, CSTA, CTCF, CTDP1, CTDSP2, CTF1, CTPS1, CTSE, CTSL, CTSS, CTTN, CUL1, CUL9, CWC22, CWF19L2, CXCL10, CXCL11, CXCL16, CXCL17, CXCR2, CXorf21, CXorf40A, CXorf40B, CXXC5, CYB5R1, CYBB, CYBRD1, CYC1, CYHR1, CYP19A1, CYP1A1, CYP24A1, CYP2J2, CYP3A5, CYP4F3, CYP7B1, CYSTM1, CYTH1, CYTIP, DAAM1, DAAM2, DAB2IP, DAPK3, DAPP1, DAXX, DBF4B, DBNDD1, DCAF12L1, DCAF13, DCAF5, DCDC2C, DCHS1, DCUN1D3, DCUN1D4, DDB1, DDB2, DDR2, DDT, DDTL, DDX23, DDX39A, DDX42, DDX5, DDX56, DDX58, DDX60, DDX60L, DENND2A, DENND3, DEPP1, DES, DGKD, DGKE, DHDDS, DHPS, DHRS9, DHX29, DHX32, DHX9, DIAPH1, DIDO1, DIP2A, DIPK2B, DISP1, DKK3, DLG4, DLK1, DLL1, DLL4, DLST, DLX2, DMBT1, DMRT1, DMRTB1, DNAAF1, DNAAF3, DNAH7, DNAJB2, DNAJC11, DNAJC7, DNASE1, DNMT1, DNPEP, DNTTIP1, DOCK1, DOCK6, DOCK9, DOK2, DOK3, DOK4, DPH1, DPH2, DPH7, DPM3, DPP7, DPT, DPYSL3, DRD2, DST, DTX3, DTX4, DUSP1, DUSP10, DUSP7, DYNLT1, DYRK2, DYRK3, E2F4, EBLN1, EBNA1BP2, ECE1, EDC3, EDC4, EDNRA, EED, EEF2, EFEMP2, EFL1, EFNA1, EFNB1, EGF, EGFL7, EGR1, EGR2, EIF1B, EIF2AK2, EIF2AK4, EIF2B4, EIF2B5, EIF2D, EIF3B, EIF3D, EIF3G, EIF3L, EIF4A1, EIF4E2, EIF4G1, ELAC2, ELP1, EMC9, EMP1, EMP2, EN2, ENDOD1, ENG, ENKD1, ENO2, ENOSF1, ENTPD6, ENTR1, EOMES, EPAS1, EPB41L1, EPC1, EPHA2, EPHA7, EPHB4, EPN2, EPOP, EPSTI1, ERBB2, ERCC1, ERRFI1, ESF1, ETS1, ETV1, EVI2A, EVI2B, EVI5, EVL, EXOC2, EXOC3, EXOSC7, EXOSC8, EZR, F2RL3, F5, F8A1, F8A3, FABP6, FAM107A, FAM110D, FAM118A, FAM126A, FAM131A, FAM13B, FAM151B, FAM160A2, FAM168B, FAM174B, FAM174C, FAM177B, FAM193A, FAM199X, FAM207A, FAM20B, FAM20C, FAM214B, FAM234A, FAM32A, FAM3A, FAM53B, FAM71D, FAM72A, FAM83G, FAM8A1, FAM9A, FAR2, FARS2, FARSA, FASTK, FASTKD2, FAXDC2, FBH1, FBP1, FBXO31, FBXO39, FBXO9, FBXW4, FBXW5, FCER1G, FCGR1A, FCGR2A, FCGR3A, FCGR3B, FCN1, FDCSP, FDPS, FER, FES, FFAR2, FGD4, FGD5, FGFR1, FGG, FGL1, FGL2, FGR, FHL1, FHL3, FHOD1, FIBP, FIS1, FKBP1A, FLAD1, FLG, FLG2, FLNA, FLNC, FLT1, FLT4, FLYWCH2, FNBP4, FOS, FOSB, FOXD3, FOXD4L1, FOXJ2, FOXK2, FOXN3, FOXO4, FOXP2, FPR1, FPR2, FREM2, FRMD6, FRYL, FXYD6, FYB1, FZD4, G6PD, GAB4, GABRA5, GADD45A, GADD45B, GADD45G, GAK, GAL, GALNT15, GALNT18, GAN, GAPT, GAS5, GAS6, GATA2, GATD3A, GBA2, GBP1, GBP3, GBP4, GBP5, GCA, GCFC2, GCH1, GCNT3, GDPD5, GEM, GFOD1, GGA1, GGA2, GGA3, GIMAP1, GIMAP6, GIMAP7, GIPC1, GJA4, GJA5, GK, GKN2, GLDN, GLG1, GLRX, GLT8D1, GMFG, GMPPA, GMPR, GNA11, GNA12, GNG11, GNG2, GNG5, GNL1, GNL2, GNLY, GOLGA3, GOLGA6L4, GOLGA8A, GOLGA8B, GON4L, GPAT4, GPD1L, GPM6B, GPN3, GPR141, GPR37L1, GPR65, GPR68, GPR84, GPRC5B, GPSM3, GPX1, GPX2, GRB10, GRB7, GRPEL2, GRSF1, GRWD1, GSDMD, GSK3A, GSN, GSS, GSTO1, GTF2B, GTF3C5, GTPBP4, GTPBP6, GTSF1, GUCD1, GUCY1A2, GUK1, H19, H2AC18, H2AC19, H2AC20, H2AC6, H2AJ, H2BC18, H2BC21, H2BC4, H2BC5, H2BC7, H4C8, HABP4, HAMP, HARS2, HAUS2, HBA1, HBA2, HBB, HBD, HBG1, HBS1L, HCAR1, HCAR2, HCFC1R1, HCK, HCST, HDAC3, HDAC7, HDLBP, HECTD1, HELB, HELZ2, HERC2, HERC5, HERC6, HERPUD1, HES1, HESX1, HEXA, HEXB, HEYL, HIF3A, HINFP, HIPK1, HIPK2, HJURP, HLA-A, HLA-B, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-DRB5, HMCES, HMGCS1, HMGN3, HMGXB3, HMOX1, HNRNPAB, HNRNPH1, HNRNPM, HOXA5, HOXB1, HP, HPGDS, HPR, HPS4, HS1BP3, HS3ST3A1, HSDL1, HSFX1, HSFX2, HSH2D, HSPA12B, HSPA2, HSPA6, HSPA8, HSPB6, HSPB7, HTR1A, HTRA3, HYAL1, HYAL2, HYOU1, ICAM2, ID2, ID3, IDH2, IDO1, IER2, IER3, IER5L, IFFO1, IFI44, IFI44L, IFI6, IFIH1, IFITI, IFITIB, IFIT2, IFIT3, IFIT5, IFITM1, IFITM2, IFITM3, IFNA10, IFNA17, IFNA21, IFNA4, IFNA6, IFNL1, IFT43, IGFBP1, IGFLR1, IGLL1, IGLL5, IGSF3, IGSF6, IL12B, IL17C, IL18RAP, ILIA, IL1B, IL1R2, ILIRN, IL27, IL2RG, IL4R, ILF3, ILKAP, ILRUN, ILVBL, IMPDH2, INAFM1, ING2, ING5, INMT, INO80E, INPP1, INPP5A, INPP5K, INSM1, INSYN2B, INTS10, INTS11, INTS3, IPO8, IQCM, IRF2, IRF7, ISG15, ISG20L2, IST1, ITGA10, ITGA5, ITGA8, ITGB3, ITGB8, ITM2A, ITM2C, ITPA, ITPKB, ITPKC, ITPR3, ITPRIP, JADE1, JAG1, JAK3, JAM3, JCAD, JCHAIN, JMJD6, JOSD2, JUN, JUND, KANK2, KAT5, KCNE1, KCNEIB, KCNJ2, KCNK17, KCNK3, KCTD10, KCTD11, KCTD12, KCTD2, KCTD20, KCTD3, KDM1A, KDM3A, KHDRBS3, KIAA0100, KIAA0355, KIAA0513, KIAA0825, KIAA0930, KIAA1671, KIF1C, KIF22, KIF3B, KIFC2, KLF10, KLF11, KLF13, KLF4, KLHDC3, KLHDC4, KLHDC7B, KLHL21, KLHL3, KLHL42, KMT2A, KMT5A, KNDC1, KPRP, KRI1, KRIT1, KRT17, KRT19, KRT72, KRT81, KSR1, LAGE3, LAMA2, LAMA4, LAMB1, LAMC3, LAMP3, LAMTOR4, LARGE1, LARP6, LAS1L, LASP1, LBH, LBP, LCE1C, LCN2, LCP1, LCP2, LDB1, LDLRAP1, LENG8, LEPR, LGALS9, LGALS9B, LGALS9C, LGI1, LGI4, LHFPL6, LIF, LIFR, LILRA1, LILRA5, LILRA6, LILRB2, LILRB3, LILRB5, LIPA, LITAF, LMANIL, LMAN2L, LMBR1L, LMNA, LMNB1, LMO2, LMOD1, LONP1, LOR, LPAR6, LPCAT4, LRATD2, LRFN1, LRFN3, LRIG1, LRPAP1, LRRC1, LRRC15, LRRC32, LRRC47, LRRC74A, LRRFIP1, LRRK2, LRRTM1, LSM7, LSS, LST1, LTF, LTO1, LUC7L, LUC7L3, LUZP1, LY6E, LY86, LY96, LYN, LYPLA1, LYRM4, LYVE1, LZTR1, LZTS1, LZTS2, MACC1, MADD, MAF1, MAFF, MAFG, MAFK, MAGEB16, MAN1B1, MAN2C1, MAP2K3, MAP2K6, MAP2K7, MAP3K14, MAP3K6, MAP3K7CL, MAP4, MAP4K5, MAPK11, MAPK9, MAPKAPK2, MARCHF2, MARCKS, MARK3, MARS1, MAST2, MAT2A, MBD3, MBIP, MCAM, MCF2L, MCM3AP, MCM7, MCTP2, MCTS1, MDC1, MDGA2, MDH1B, ME3, MED11, MED15, MED18, MED24, MEDAG, MEF2D, MEIS1, MEPCE, METTL17, METTL3, METTL7A, METTL7B, MFAP1, MFGE8, MFN2, MFNG, MFSD6, MGAM, MGAT5B, MGLL, MICAL1, MICB, MIER1, MIF4GD, MINK1, MLLT10, MLNR, MLXIP, MMAB, MMP1, MMP10, MMP12, MMP14, MMP25, MMP28, MMP8, MNDA, MOAP1, MOB2, MON2, MORC2, MPHOSPH10, MPHOSPH8, MPLKIP, MPPED1, MPRIP, MPV17, MPZL1, MRFAP1L1, MRNIP, MRPL11, MRPL28, MRPL44, MRPL55, MRPS2, MRTFA, MS4A15, MS4A3, MSTO1, MTA2, MTA3, MTCH1, MT-CO1, MT-CO2, MT-CO3, MTFR1L, MTHFR, MT1F3, MTLN, MTURN, MTX1, MUC5AC, MUL1, MVP, MX1, MX2, MXD1, MXD4, MXRA7, MYADM, MYBBP1A, MYC, MYCBP2, MYCT1, MYL1, MYO15B, MYO1D, MYO1G, MYO9B, MYOM2, MYOZ2, MYZAP, MZB1, MZT2B, NAA10, NAA35, NAA38, NAA60, NAB2, NADSYN1, NAP1L4, NASP, NAT10, NAT9, NBL1, NBN, NBPF26, NCALD, NCAPH2, NCBP2AS2, NCF4, NCKIPSD, NCR1, NDNF, NDRG1, NDRG2, NDST1, NDST2, NDUFA4L2, NDUFAB1, NDUFS2, NDUFS6, NDUFS8, NDUFV1, NEBL, NECAP1, NEIL2, NEK7, NELFA, NELFB, NELFE, NEMP2, NES, NETO1, NEXN, NF2, NFATC2, NFATC4, NFKBID, NFRKB, NFX1, NIBAN2, NIPAL3, NISCH, NKD1, NKPD1, NLE1, NLRP1, NME1, NMI, NMRAL1, NOC2L, NOD1, NOL4, NOL8, NOP10, NOP16, NOP53, NOP56, NOP9, NORAD, NOSIP, NOTCH2, NOTCH4, NOTO, NPC1, NPIPB11, NPIPB12, NPIPB13, NPIPB3, NPIPB4, NPIPB5, NPR1, NPR3, NR1D2, NR2C2, NR2C2AP, NR4A1, NRBP1, NRIP1, NSD2, NSUN4, NT5C3A, NT5DC2, NTNG2, NTRK2, NUAK1, NUDCD3, NUMA1, NUP188, NUPR1, NYNRIN, NYX, OAS1, OAS2, OAS3, OASL, OBSCN, ODC1, OLIG1, OLR1, ONECUT1, OR13G1, OR2AT4, OR2C1, ORAI2, OS9, OSBPL10, OSGEP, OTUD3, OTUD7B, OTULINL, OTX1, OXCT1, P2RY13, P2RY14, P3H1, P4HB, PACS2, PACSIN2, PACSIN3, PADI2, PADI4, PAK1, PALD1, PALMD, PAMR1, PAN2, PAPPA, PAQR9, PARD3, PARL, PARP2, PARP9, PARVB, PATL1, PAX9, PAXX, PBXIP1, PCAT1, PCBP1, PCDH1, PCDH12, PCGF3, PCGF5, PCID2, PCNX3, PCSK9, PCTP, PDCD11, PDE2A, PDE4B, PDE9A, PDGFB, PDGFRB, PDGFRL, PDIA5, PDIA6, PDK4, PDLIM3, PDLIM4, PDPK1, PDRG1, PDXK, PEAK1, PELI1, PELO, PER1, PER3, PEX5, PFKL, PFN1, PGAM4, PGAP6, PGF, PGLYRP1, PHC2, PHF11, PHLDA2, PHLDA3, PHLDB1, PHPT1, PI4K2A, PI4K2B, PI4KA, PI4KB, PIAS3, PIEZO1, PIGR, PIGU, PIH1D1, PIK3AP1, PIK3IP1, PIK3R4, PILRA, PIM2, PIN4, PIP4P1, PISD, PJA1, PKLR, PKN1, PLA2G7, PLAAT2, PLAAT3, PLAC8, PLAC9, PLBD1, PLCD1, PLCG1, PLEK, PLEKHA4, PLEKHG3, PLEKHJ1, PLEKHM1, PLEKHM2, PLEKHO1, PLEKHO2, PLEKHS1, PLK2, PLLP, PLP2, PLPP1, PLPP3, PLSCR4, PLXNA2, PLXNB1, PLXNB2, PLXND1, PML, PMPCB, PNISR, PNLDC1, PNMA5, PNP, PNRC1, PODN, PODXL, POFUT2, POLDIP3, POLR1E, POLR2D, POLR2K, POLR3C, POLR3GL, POM121C, POMT2, POMZP3, POP5, POU2AF1, POU6F1, PPARGC1B, PPDPF, PPIB, PPID, PPIG, PPIH, PPM1F, PPM1M, PPPI1CA, PPP1R12A, PPP1R12C, PPP1R13B, PPP1R14A, PPP1R14B, PPP1R16B, PPP1R3C, PPP2R5B, PPP3R1, PPP6R2, PPRC1, PQBP1, PRDM2, PRDM8, PRDX1, PRDX2, PRELID1, PRKAB1, PRKAR1B, PRKAR2A, PRKX, PRMT1, PRMT7, PRMT9, PROK2, PRPF39, PRPF6, PRR13, PRR14L, PRR3, PRR36, PRSS16, PRX, PSENEN, PSMA4, PSMB1, PSMB10, PSMB4, PSMC1, PSMC3, PSMC5, PSMC6, PSMD2, PSMD4, PSMD6, PSMD7, PSMD8, PSME3, PSTPIP2, PTCD3, PTDSS2, PTGDS, PTGIS, PTH1R, PTK2B, PTK7, PTMS, PTP4A3, PTP A, PTPN1, PTPN13, PTPN3, PTPRC, PTPRM, PTPRZ1, PUF60, PUS1, PVR, PWP2, PWWP2A, PWWP3A, PWWP3B, PXDC1, PXDN, PXN, PYCR2, PYGO2, QARS1, QSOX1, QTRT1, R3HCC1, RAB11FIP3, RAB34, RAB4A, RAB8B, RABGAP1L, RABGGTA, RAC2, RACK1, RAF1, RAI2, RALGDS, RAMP3, RANBP10, RANBP3, RANGAP1, RAPGEF1, RAPGEF3, RARRES2, RASA3, RASD2, RASGEF1B, RASGEF1C, RASIP1, RASL11A, RASL12, RASSF1, RASSF10, RBFOX2, RBM10, RBM11, RBM19, RBM33, RBM6, RBP4, RCAN1, RCC2, RCE1, RCN2, RCOR1, RECK, REPS2, RETREG3, REV3L, REX1BD, RFC1, RFLNB, RFTN1, RFXANK, RGCC, RGL4, RGP1, RGPD1, RGPD2, RGPD3, RGPD4, RGPD5, RGPD6, RGS12, RGS18, RGS3, RGS4, RHBDD2, RHBDF1, RHOC, RHOH, RIMS3, RIOK2, RIPOR2, RMDN1, RMND5A, RMND5B, RNASE2, RND1, RND3, RNF113A, RNF122, RNF144A, RNF149, RNF152, RNF168, RNF175, RNF185, RNF19B, RNF25, RNF4, RNF40, RNMT, RNPS1, RNU4ATAC, ROBO3, ROBO4, RP2, RPAIN, RPH3A, RPIA, RPL13, RPL18, RPL3, RPL36AL, RPL8, RPLP0, RPRD1A, RPS19BP1, RPS28, RPS5, RPS6KA2, RPS9, RPSA, RPTOR, RRAD, RRP1, RRP12, RRP7A, RSAD1, RSAD2, RTKN2, RTN3, RTP4, RUVBL2, RXRB, S100A11, S100A12, S100A13, S100A16, S100A2, S100A8, S100A9, S100P, S100PBP, S1PR2, SAA1, SAA2, SAE1, SAFB, SAFB2, SAMD9, SAMD9L, SAMSN1, SARS1, SASH1, SAT1, SCAF4, SCAMP4, SCGB1A1, SCN2A, SCN4B, SCN7A, SCNN1G, SCP2D1, SCRN2, SCYL1, SDC3, SDHAF1, SEC16A, SEC23A, SEC23IP, SELENBP1, SELL, SELP, SEM1, SEMA3B, SEMA3F, SEMA4C, SEMA6B, SENP3, SENP5, SEPHS1, SEPTIN14, SEPTIN8, SEPTIN9, SERF2, SERPINA1, SERPINB2, SERPINB6, SERPINB9, SERPINE2, SERTAD1, SERTAD3, SESN2, SEZ6L2, SF3A2, SF3B1, SF3B4, SF3B5, SFN, SFRP2, SFT2D1, SFTPC, SGCA, SGIP1, SGK1, SGSM2, SGTA, SH3BGRL3, SH3BP5, SH3D19, SH3PXD2A, SH3PXD2B, SH3RF1, SH3TC1, SHANK3, SHC2, SHE, SHFL, SHOC1, SIDT2, SIGLEC14, SIGLEC5, SIK2, SIRPB1, SIRT1, SIVA1, SKIV2L, SKOR1, SLAMF7, SLC24A4, SLC25A23, SLC25A25, SLC25A29, SLC25A3, SLC25A30, SLC25A36, SLC25A4, SLC25A44, SLC25A6, SLC26A8, SLC30A4, SLC35A4, SLC35B2, SLC35F1, SLC35F2, SLC35G2, SLC38A5, SLC39A7, SLC39A8, SLC41A3, SLC44A2, SLC5A7, SLC66A2, SLC6A8, SLC9A1, SLCO2B1, SLF2, SLIT2, SLIT3, SLK, SMAD7, SMAP2, SMARCA4, SMARCB1, SMARCD2, SMC3, SMG5, SMIM25, SMIM27, SMIM3, SMPD4, SMTN, SMURF1, SNAH, SNAPC2, SNCG, SNHG3, SNRNP200, SNRNP70, SNRPA1, SNX10, SNX11, SNX25, SOCS1, SOCS2, SOGA1, SOS1, SP110, SP140, SP140L, SPAG6, SPARCL1, SPATA16, SPATA31E1, SPEM2, SPG7, SPHK1, SPH, SPOUT1, SPRED1, SPRR2E, SPRYD3, SPTLC2, SQSTM1, SREK1, SRGN, SRSF5, SRSF7, SSH1, SSNA1, ST6GAL1, ST6GAL2, ST6GALNAC4, ST8SIA2, STAB1, STAG1, STAP1, STAP2, STARD3, STARD8, STARD9, STAT1, STAT2, STAT4, STAT5A, STC1, STEAP1, STEAP4, STK16, STK25, STK38, STK40, STN1, STRIP1, STRN4, STUB1, STX11, STXBP6, STYX, SUCNR1, SUGP1, SULT1A1, SULT1A2, SULT1B1, SUN1, SUN3, SUN5, SUPT6H, SURF1, SURF6, SYAP1, SYN1, SYNE1, SYNM, SYNPO, SYNPO2L, SYT11, TACC1, TAF1, TAFA2, TAGAP, TAGLN, TANC1, TANC2, TAOK3, TAPI, TARBP2, TARS3, TATDN2, TAZ, TBC1D17, TBC1D2B, TBC1D9, TBC1D9B, TBCEL, TBP, TBX2, TCEA3, TCEAL9, TCERG1, TCF21, TCF24, TCF25, TCF7L1, TCN1, TEAD3, TECPR1, TEF, TET2, TEX10, TEX264, TEX9, TFEC, TFIP11, TFPI2, TGFBR1, TGFBR2, THAP2, THAP7, THBD, THBS3, THEM4, THOC6, THSD7B, THUMPD3, TIMM13, TIMM23, TIMM44, TIMP3, TINAGL1, TJAP1, TLE3, TLE4, TLR1, TLR7, TM4SF20, TMBIM1, TMC6, TMEM100, TMEM109, TMEM125, TMEM154, TMEM171, TMEM176B, TMEM200B, TMEM208, TMEM235, TMEM245, TMEM252, TMEM255B, TMEM39B, TMEM45B, TMEM51, TMEM52B, TMEM71, TMEM74B, TMEM88, TMOD1, TMPRSS2, TMTC1, TNF, TNFAIP1, TNFAIP6, TNFRSF10B, TNFRSF14, TNFSF10, TNFSF13B, TNFSF14, TNFSF8, TNIK, TNIP2, TNIP3, TNNC1, TNS1, TNS2, TNXB, TOE1, TOLLIP, TOM1L2, TOMM34, TOP2A, TOR1B, TP53BP1, TP53BP2, TP73, TPCN1, TPD52L2, TPP1, TPRG1L, TPSAB1, TPSB2, TPST1, TRAF2, TRAF5, TRAK1, TRAK2, TRAPPC10, TREM1, TREML4, TRGC1, TRIB3, TRIM21, TRIM22, TRIM29, TRIM38, TRIM5, TRIM69, TRIO, TRIP10, TRIR, TRIT1, TRMT61A, TRNAU1AP, TRPC4AP, TRPC6, TRPM5, TRPM8, TRRAP, TSC1, TSC22D3, TSFM, TSPAN18, TSPAN4, TSPAN9, TSPYL2, TSR1, TSSC4, TTC14, TTC31, TTC7A, TTL, TUBA1A, TUBA1B, TUBA1C, TUBA4A, TUBB2A, TUBB2B, TUBB4B, TUBB6, TUBGCP2, TUBGCP3, TUBGCP6, TULP3, TUSC7, TUT4, TWF2, TWNK, TXLNA, TXNDC11, TYROBP, UACA, UBA7, UBB, UBC, UBE2J2, UBE2L6, UBIAD1, UBL4A, UBR4, UBTF, UBXN1, UCP2, UNC13B, UNC80, UNC93A, UPK2, UPK3B, UPP1, UQCC2, UQCRC1, URB1, URGCP, URM1, UROD, USB1, USP15, USP18, USP19, USP20, USP22, USP30, USP40, USP47, USP53, USP7, UTP14C, UTP20, UTP6, VASN, VASP, VAX1, VCPKMT, VIPR1, VLDLR, VNN2, VOPP1, VPS11, VPS13D, VPS16, VPS18, VPS28, VPS37B, VPS39, VPS8, VSIG10L, VSIG2, VSTM4, VWA7, VWF, WAS, WASHC1, WBP1L, WDR13, WDR37, WDR43, WDR74, WDR75, WDR91, WIPF1, WIPI1, WIPI2, WNT2B, XAB2, XAF1, XAGE1A, XAGE1B, XKR9, XPC, XPO5, XRCC6, XRN1, YARS1, YKT6, YPEL3, ZBP1, ZBTB10, ZBTB17, ZBTB34, ZBTB44, ZBTB5, ZC3H7B, ZC3HAV1, ZCCHC24, ZCCHC7, ZDHHC11B, ZDHHC19, ZDHHC7, ZFAND2B, ZFP36L2, ZFYVE19, ZMYM2, ZNF106, ZNF133, ZNF154, ZNF160, ZNF263, ZNF3, ZNF320, ZNF330, ZNF331, ZNF384, ZNF385A, ZNF385D, ZNF394, ZNF395, ZNF426, ZNF451, ZNF480, ZNF496, ZNF513, ZNF585B, ZNF599, ZNF622, ZNF692, ZNF697, ZNF761, ZNF83, ZNF841, ZNRD2, ZNRF4, ZPLD1, ZRANB1, ZRSR2, ZSCAN18, ZSWIM7, ZSWIM8, ZZEF1 BAL-CoV2 to PBMC-CoV2 (8,959 DEGs in Airway) A2M, A2ML1, A4GNT, AAAS, AACS, AADAT, AAGAB, AAMP, AANAT, AARS2, AASDHPPT, AASS, AATF, AATK, ABCA1, ABCA12, ABCA13, ABCA2, ABCA3, ABCA5, ABCA6, ABCA7, ABCB1, ABCB10, ABCB11, ABCB7, ABCB8, ABCB9, ABCC1, ABCC10, ABCC2, ABCC3, ABCC4, ABCD1, ABCD2, ABCD3, ABCD4, ABCE1, ABCF2, ABCF3, ABCG1, ABCG8, ABHD10, ABHD12, ABHD12B, ABHD13, ABHD16A, ABHD17A, ABHD17B, ABHD17C, ABHD2, ABHD3, ABHD6, ABHD8, ABH, ABI3BP, ABITRAM, ABL1, ABL2, ABT1, ABTB1, ACAA1, ACAA2, ACACB, ACAD10, ACAD8, ACAD9, ACADL, ACADM, ACADS, ACADSB, ACADVL, ACAP1, ACAP2, ACAP3, ACAT1, ACBD3, ACBD4, ACBD5, ACCS, ACD, ACE, ACE2, ACHE, ACIN1, ACLY, ACO1, ACO2, ACOD1, ACOT1, ACOT11, ACOT13, ACOT2, ACOT4, ACOT7, ACOT8, ACOX1, ACOX2, ACOX3, ACP2, ACP5, ACPP, ACRBP, ACSF3, ACSL4, ACSL5, ACSL6, ACSM3, ACSM6, ACSS1, ACSS2, ACSS3, ACTB, ACTG1, ACTL6A, ACTN4, ACTR1A, ACTR1B, ACTR2, ACTR3C, ACVR1, ACVR1C, ACVR2A, ACVRL1, ACYP2, ADA2, ADAM10, ADAM15, ADAM19, ADAM22, ADAM28, ADAM32, ADAM8, ADAMDEC1, ADAMTS10, ADAMTS19, ADAMTS2, ADAMTS9, ADAMTSL4, ADAP1, ADARB1, ADCK1, ADCK2, ADCK5, ADCY2, ADCY3, ADCY6, ADCY7, ADCY9, ADD1, ADD2, ADD3, ADGB, ADGRA2, ADGRE3, ADGRE5, ADGRF1, ADGRF5, ADGRG1, ADGRG3, ADGRG5, ADGRG6, ADGRL1, ADGRL2, ADGRV1, ADH1B, ADH1C, ADH5, ADH6, ADH7, ADHFE1, ADIPOR1, ADIPOR2, ADM, ADNP, ADNP2, ADORA1, ADORA3, ADPGK, ADPRHL1, ADPRM, ADRM1, ADSL, ADSS1, ADTRP, AEBP1, AEN, AFAP1L2, AFDN, AFF2, AFF3, AFF4, AFG1L, AFG3L2, AGAP1, AGAP2, AGAP4, AGAP6, AGAP9, AGBL2, AGBL5, AGER, AGFG1, AGFG2, AGGF1, AGMAT, AGO1, AGO2, AGO4, AGPAT1, AGPAT2, AGPAT3, AGPS, AGR2, AGR3, AGRN, AGRP, AGTPBP1, AGTRAP, AHDC1, AHU, AHNAK, AHSA1, AHSP, AICDA, AIF1, AIFM1, AIG1, AIM2, AIP, AJM1, AK1, AK4, AK6, AK7, AK9, AKAP1, AKAP11, AKAP12, AKAP13, AKAP14, AKAP17A, AKAP3, AKAP5, AKAP6, AKAP7, AKAP8, AKAP8L, AKAP9, AKIRIN1, AKIRIN2, AKNA, AKR1A1, AKR1B1, AKR1C1, AKR1C2, AKR1C3, AKR1C4, AKR7A2, AKT1, AKT1S1, AKT2, AKT3, AKTIP, ALAD, ALAS1, ALAS2, ALCAM, ALDH16A1, ALDH1A1, ALDH1A2, ALDH1A3, ALDH1B1, ALDH2, ALDH3A1, ALDH3A2, ALDH3B1, ALDH3B2, ALDH4A1, ALDH6A1, ALDH7A1, ALDOA, ALG1, ALG12, ALG14, ALG2, ALG6, ALG9, ALK, ALKBH1, ALKBH4, ALKBH5, ALKBH6, ALMS1, ALOX12, ALOX12B, ALOX15, ALOX5AP, ALPK3, ALYREF, AMDHD2, AMER1, AMFR, AMOTL1, AMOTL2, AMPD2, AMPD3, AMY1B, AMY2A, AMY2B, AMZ2, ANAPC10, ANAPC11, ANAPC13, ANAPC15, ANAPC2, ANAPC4, ANAPC5, ANGPT4, ANGPTL1, ANK1, ANK2, ANK3, ANKDD1A, ANKFN1, ANKH, ANKHD1, ANKHD1-EIF4EBP3, ANKIB1, ANKLE2, ANKMY1, ANKMY2, ANKRA2, ANKRD10, ANKRD12, ANKRD13A, ANKRD13D, ANKRD17, ANKRD18B, ANKRD22, ANKRD26, ANKRD27, ANKRD28, ANKRD29, ANKRD34B, ANKRD35, ANKRD36B, ANKRD39, ANKRD46, ANKRD50, ANKRD52, ANKRD54, ANKRD55, ANKRD6, ANKRD65, ANKRD66, ANKRD9, ANKS1A, ANKUB1, ANKZF1, ANO10, ANO5, ANO6, ANO8, ANO9, ANOS1, ANP32A, ANP32B, ANPEP, ANTXR1, ANTXR2, ANXA1, ANXA11, ANXA2, ANXA3, ANXA4, ANXA5, ANXA6, AOAH, AOC2, AOC3, AOPEP, AOX1, AP1AR, AP1B1, AP1G2, AP1M1, AP1S1, AP1S2, AP2A1, AP2M1, AP3B1, AP3M1, AP3S2, AP4B1, AP4E1, AP5B1, AP5Z1, APAF1, APBA1, APBA2, APBA3, APBB1, APBBHP, APBB2, APBB3, APC, APC2, APEH, APELA, APEX2, APH1A, APIP, APLF, APLP2, APMAP, APOBEC3B, APOBEC3C, APOBEC3F, APOBEC4, APOBR, APOC1, APOE, APOL2, APOL3, APOL4, APOM, APOO, APOOL, APP, APPL2, APRT, APTX, AQP10, AQP4, AQP5, AQR, AR, ARAF, ARAP1, ARAP3, ARCN1, AREG, ARF1, ARF3, ARF5, ARFGAP1, ARFGAP2, ARFGAP3, ARFGEF1, ARFGEF3, ARFIP1, ARFRP1, ARGLU1, ARHGAP1, ARHGAP10, ARHGAP11A, ARHGAP12, ARHGAP15, ARHGAP18, ARHGAP19, ARHGAP21, ARHGAP25, ARHGAP27, ARHGAP30, ARHGAP32, ARHGAP33, ARHGAP4, ARHGAP42, ARHGAP44, ARHGAP5, ARHGAP6, ARHGAP9, ARHGDIA, ARHGDIB, ARHGEF1, ARHGEF16, ARHGEF18, ARHGEF19, ARHGEF2, ARHGEF28, ARHGEF3, ARHGEF35, ARHGEF38, ARHGEF39, ARHGEF40, ARHGEF6, ARHGEF7, ARID1A, ARID1B, ARID2, ARID3A, ARID3B, ARID4A, ARID5A, ARIH1, ARIH2, ARL1, ARL10, ARL13B, ARL14, ARL14EP, ARL15, ARL16, ARL17A, ARL2BP, ARL3, ARL4A, ARL4C, ARL5A, ARL6, ARL6IP6, ARL8A, ARL8B, ARMC2, ARMC3, ARMC4, ARMC5, ARMC6, ARMC7, ARMC8, ARMC9, ARMCX1, ARMCX2, ARMCX4, ARMH1, ARMH3, ARMT1, ARNTL, ARNTL2, ARPCIA, ARPC1B, ARPC2, ARPC3, ARPC4, ARPP19, ARRB2, ARRDC1, ARRDC2, ARSA, ARSD, ARSG, ARV1, ARVCF, ASAP3, ASB1, ASB6, ASB8, ASCC1, ASCC2, ASCC3, ASF1A, ASF1B, ASGR1, ASGR2, ASH1L, ASIC3, ASL, ASMTL, ASPH, ASPHD2, ASPN, ASPSCR1, ASRGL1, ASS1, ASTN2, ASXL1, ASXL2, ASXL3, ATAD2, ATAD2B, ATAD3A, ATAD3B, ATAD3C, ATF1, ATF2, ATF3, ATF4, ATF6, ATF6B, ATF7IP, ATG101, ATG12, ATG13, ATG14, ATG16L2, ATG2A, ATG2B, ATG3, ATG4A, ATG4B, ATG4C, ATG4D, ATG5, ATG7, ATG9A, ATL2, ATL3, ATM, ATMIN, ATOX1, ATP10A, ATP10B, ATP11A, ATP12A, ATP13A1, ATP13A2, ATP13A3, ATP1A1, ATP1B1, ATP1B4, ATP23, ATP2A2, ATP2A3, ATP2B1, ATP2B2, ATP2B4, ATP2C2, ATP5F1A, ATP5F1B, ATP5F1C, ATP5F1D, ATP5F1E, ATP5IF1, ATP5MC1, ATP5MC2, ATP5MC3, ATP5MD, ATP5ME, ATP5MF, ATP5MG, ATP5MPL, ATP5PB, ATP5PD, ATP5PF, ATP5PO, ATP6AP1, ATP6AP1L, ATP6AP2, ATP6V0A2, ATP6V0A4, ATP6V0B, ATP6V0C, ATP6V0D1, ATP6V0D2, ATP6V0E1, ATP6V0E2, ATP6V1A, ATP6V1C1, ATP6V1D, ATP6V1E1, ATP6V1F, ATP6V1G1, ATP6V1H, ATP7A, ATP7B, ATP8A1, ATP8B1, ATP8B2, ATP8B3, ATP9A, ATPAF1, ATPAF2, ATXN1L, ATXN2, ATXN2L, ATXN3, ATXN7, ATXN7L1, ATXN7L3, ATXN7L3B, AUH, AUP1, AURKA, AURKB, AUTS2, AVEN, AVPI1, AXIN1, AXL, AZGP1, AZI2, AZIN2, AZU1, B2M, B3GALNT1, B3GALNT2, B3GALT5, B3GALT6, B3GAT1, B3GAT3, B3GNT2, B3GNT3, B3GNT5, B3GNT7, B3GNT8, B3GNTL1, B4GALT2, B4GALT3, B4GALT4, BACE2, BACH2, BAD, BAG2, BAG3, BAG6, BAHCC1, BAHD1, BAIAP2L1, BAK1, BANF1, BANK1, BANP, BAP1, BATF3, BAX, BAZ1A, BAZ1B, BAZ2A, BAZ2B, BBC3, BBIP1, BBS10, BBS12, BBS2, BBS9, BBX, BCAM, BCAP29, BCAP31, BCAR3, BCAS1, BCAS2, BCAT1, BCCIP, BCKDHA, BCKDHB, BCKDK, BCL11B, BCL2A1, BCL2L1, BCL2L11, BCL2L14, BCL2L15, BCL3, BCL6, BCL9L, BCLAF1, BCLAF3, BCOR, BCORL1, BCR, BDH2, BDKRB2, BDP1, BECN1, BEND2, BEND4, BEND5, BEND7, BEST3, BET1, BET1L, BEX1, BFSP1, BHLHA15, BHLHE40, BHLHE41, BICD1, BICD2, BICDL2, BICRA, BICRAL, BIN1, BIN2, BIN3, BIRC3, BIRC5, BLK, BLNK, BLOC1S1, BLOC1S2, BLOC1S4, BLOC1S5, BLOC1S6, BLVRA, BLZF1, BMF, BMP2K, BMP3, BMP6, BMPR1A, BMPR1B, BMPR2, BMS1, BMX, BNIP1, BNIP3, BNIP3L, BOD1, BOLA1, BOLA2B, BOLA3, BOP1, BORCS5, BORCS6, BORCS7, BORCS8, BPGM, BPHL, BPIFA1, BPIFB1, BPIFB4, BPTF, BRAT1, BRCA1, BRCA2, BRCC3, BRD1, BRD2, BRD8, BRD9, BRF1, BRF2, BRI3, BRI3BP, BRMS1, BRPF1, BRPF3, BRWD1, BSCL2, BSDC1, BSG, BSPRY, BST1, BST2, BTAF1, BTBD1, BTBD10, BTBD11, BTBD19, BTBD2, BTBD3, BTBD7, BTBD8, BTF3, BTF3L4, BTG1, BTG2, BTK, BTLA, BTN2A1, BTN3A1, BTN3A2, BTNL9, BTRC, BUD13, BUD23, BZW1, BZW2, C10orf143, C10orf25, C10orf67, C11orf1, C11orf16, C11orf21, C11orf24, C11orf45, C11orf65, C11orf68, C11orf71, C11orf74, C11orf88, C11or97, C12orf10, C12orf4, C12orf43, C12orf45, C12orf49, C12orf60, C12orf73, C12orf74, C13orf46, C14orf119, C15orf39, C15orf40, C15orf48, C15orf62, C15orf65, C16orf54, C16orf58, C16orf70, C16orf72, C16orf74, C16orf87, C16orf89, C16orf91, C17orf100, C17orf49, C17orf58, C17orf80, C17orf97, C18orf21, C18orf25, C18orf32, C18orf54, C19orf25, C19orf38, C19orf47, C19orf53, C19orf54, C19orf71, C1D, C1GALT1, C1GALT1C1, C1orf115, C1orf116, C1orf122, C1orf131, C1orf141, C1orf158, C1orf159, C1orf162, C1orf189, C1orf194, C1orf198, C1orf21, C1orf216, C1orf50, C1orf53, C1orf54, C1orf87, C1QA, C1QB, C1QC, C1QTNF6, C1RL, C2, C20orf194, C20orf85, C20or96, C21or91, C2CD2L, C2orf15, C2orf42, C2orf49, C2orf68, C2orf73, C2orf76, C2orf88, C2or92, C3, C3AR1, C3orf14, C3orf18, C3orf49, C3orf62, C3orf67, C3orf84, C4A, C4B, C4orf19, C4orf3, C4orf46, C5AR1, C5AR2, C5orf22, C5orf24, C5orf30, C5orf49, C5orf51, C5orf58, C6, C6orf120, C6orf132, C6orf136, C6orf163, C6orf226, C6orf47, C6orf62, C6orf89, C7orf26, C7orf50, C7orf57, C8B, C8orf34, C8orf37, C9orf116, C9orf129, C9orf135, C9orf139, C9orf152, C9orf16, C9orf24, C9orf64, C9orf78, CA1, CA13, CA14, CA2, CA4, CA5B, CA8, CAAP1, CABCOCO1, CABIN1, CABLES1, CABLES2, CABP4, CACHD1, CACNA1E, CACNA1F, CACNA1I, CACNA2D1, CACNA2D2, CACNA2D3, CACNA2D4, CACNB1, CACTIN, CACUL1, CACYBP, CAD, CADPS2, CALCOCO2, CALCR, CALHM2, CALHM5, CALHM6, CALM1, CALM2, CALM3, CALU, CAMK1, CAMK1D, CAMK2D, CAMK2G, CAMK2N1, CAMK4, CAMKK1, CAMKK2, CAMLG, CAMP, CAMSAP2, CAMTA1, CAMTA2, CANT1, CAP1, CAP2, CAPN1, CAPN10, CAPN12, CAPN13, CAPN15, CAPN2, CAPN3, CAPN5, CAPN7, CAPNS1, CAPRIN1, CAPS2, CAPSL, CAPZAI, CAPZB, CARD11, CARD19, CARD6, CARD8, CARD9, CARF, CARHSP1, CARM1, CARMIL1, CARMIL2, CARMIL3, CARNMT1, CARNS1, CASC1, CASC3, CASC4, CASK, CASKIN2, CASP3, CASP4, CASP5, CASP7, CASP8, CASP8AP2, CASS4, CASTOR2, CASZ1, CATSPER1, CATSPERB, CATSPERD, CAV3, CAVIN1, CAVIN2, CAVIN4, CBFA2T2, CBFA2T3, CBL, CBLL1, CBR1, CBS, CBSL, CBWD6, CBX1, CBX3, CBX4, CBX6, CBX7, CBY1, CC2D1A, CC2D1B, CC2D2A, CCAR1, CCAR2, CCDC102B, CCDC106, CCDC107, CCDC110, CCDC112, CCDC113, CCDC117, CCDC124, CCDC125, CCDC127, CCDC130, CCDC134, CCDC137, CCDC138, CCDCM1, CCDCM6, CCDC15, CCDC158, CCDC159, CCDC160, CCDC167, CCDC17, CCDC170, CCDC171, CCDC178, CCDC18, CCDC180, CCDC181, CCDC186, CCDC187, CCDC190, CCDC200, CCDC22, CCDC25, CCDC28B, CCDC30, CCDC32, CCDC33, CCDC34, CCDC36, CCDC40, CCDC51, CCDC57, CCDC58, CCDC6, CCDC60, CCDC61, CCDC65, CCDC66, CCDC69, CCDC7, CCDC71, CCDC71L, CCDC74A, CCDC74B, CCDC78, CCDC80, CCDC81, CCDC85B, CCDC85C, CCDC88A, CCDC88B, CCDC88C, CCDC89, CCDC9, CCDC90B, CCDC91, CCDC92, CCDC97, CCDC9B, CCHCR1, CCL18, CCL2, CCL20, CCL23, CCL3, CCL3L1, CCL4, CCL4L2, CCL5, CCL7, CCL8, CCM2, CCN1, CCN2, CCNB2, CCNB3, CCND1, CCND2, CCND3, CCNDBP1, CCNE2, CCNF, CCNG2, CCNI, CCNJL, CCNK, CCNL1, CCNL2, CCNO, CCNT1, CCNY, CCNYL1, CCP110, CCR1, CCR4, CCR5, CCR7, CCRL2, CCS, CCSAP, CCSER2, CCT7, CCZ1B, CD101, CD14, CD160, CD164, CD180, CD19, CD1A, CD1C, CD1D, CD2, CD200, CD22, CD226, CD24, CD244, CD247, CD27, CD274, CD276, CD28, CD2AP, CD2BP2, CD300A, CD300C, CD300H, CD300LB, CD33, CD36, CD37, CD3D, CD3E, CD3EAP, CD3G, CD4, CD40LG, CD44, CD46, CD47, CD48, CD5, CD52, CD53, CD59, CD5L, CD6, CD68, CD69, CD7, CD72, CD79A, CD79B, CD80, CD81, CD82, CD84, CD8A, CD8B, CD8B2, CD9, CD93, CD96, CD99, CD99L2, CDA, CDADC1, CDAN1, CDC123, CDC14A, CDC14B, CDC20, CDC20B, CDC25A, CDC25B, CDC26, CDC27, CDC34, CDC37, CDC37L1, CDC42BPA, CDC42BPB, CDC42EP1, CDC42EP2, CDC42EP3, CDC42EP4, CDC42SE1, CDC42SE2, CDC5L, CDC6, CDC7, CDC73, CDCA3, CDCA4, CDCA5, CDCA7L, CDCA8, CDCP1, CDH13, CDH23, CDH26, CDHR3, CDIP1, CDIPT, CDK10, CDK11A, CDK11B, CDK13, CDK14, CDK16, CDK2, CDK20, CDK2AP1, CDK4, CDK5R1, CDK5RAP2, CDK5RAP3, CDK6, CDK7, CDK9, CDKAL1, CDKL5, CDKN1A, CDKN1C, CDKN2AIP, CDKN2B-AS1, CDKN2D, CDPF1, CDR2, CDS1, CDS2, CDV3, CDYL, CDYL2, CEACAM1, CEACAM19, CEACAM3, CEACAM4, CEACAM5, CEACAM6, CEACAM7, CEBPA, CEBPB, CEBPZ, CELF1, CELF2, CELSR1, CELSR2, CELSR3, CEMIP, CEMIP2, CENPB, CENPBD1, CENPH, CENPK, CENPL, CENPO, CENPP, CENPQ, CENPS, CENPW, CEP112, CEP126, CEP128, CEP162, CEP170, CEP19, CEP192, CEP250, CEP290, CEP295NL, CEP350, CEP68, CEP70, CEP76, CEP78, CEP83, CEP85, CEP85L, CEP89, CEP95, CERK, CERKL, CERS2, CERS4, CERS5, CERS6, CERT1, CES2, CES3, CES4A, CETN2, CETN3, CFAP20, CFAP221, CFAP298, CFAP300, CFAP36, CFAP410, CFAP43, CFAP44, CFAP45, CFAP47, CFAP52, CFAP53, CFAP54, CFAP57, CFAP61, CFAP65, CFAP70, CFAP97D2, CFDP1, CFH, CFL1, CFL2, CFLAR, CFP, CFTR, CGAS, CGGBP1, CGN, CGNL1, CHAF1A, CHCHD1, CHCHD10, CHCHD3, CHCHD6, CHCHD7, CHD1, CHD2, CHD3, CHD4, CHD6, CHD8, CHD9, CHDH, CHEK1, CHEK2, CHERP, CHFR, CHIC1, CHIC2, CHID1, CHKB, CHL1, CHM, CHMP1A, CHMPIB, CHMP2A, CHMP2B, CHMP4A, CHMP4B, CHMP4C, CHMP5, CHMP6, CHMP7, CHN2, CHP1, CHP2, CHPF, CHPF2, CHPT1, CHRDL2, CHRFAM7A, CHRNA2, CHRNA3, CHRNA7, CHST10, CHST11, CHST12, CHST13, CHST15, CHST2, CHST4, CHST6, CHST9, CHSY1, CHTF18, CHTF8, CHTOP, CHURC1, CIAO1, CIAO2A, CIAO3, CIAPIN1, CIC, CIITA, CIPC, CIR1, CIRBP, CISD1, CITED4, CIZ1, CKAP2, CKAP2L, CKAP4, CKAP5, CKB, CKLF, CKMT1A, CKMT1B, CKMT2, CKS2, CLASP1, CLASRP, CLC, CLCA2, CLCA4, CLCF1, CLCN2, CLCN3, CLCN5, CLCN6, CLCN7, CLDN1, CLDN10, CLDN12, CLDN15, CLDN16, CLDN18, CLDN23, CLDN3, CLDN4, CLDN5, CLDN9, CLDND1, CLDND2, CLEC11A, CLEC12A, CLEC12B, CLEC17A, CLEC18A, CLEC1B, CLEC2D, CLEC4A, CLEC4D, CLEC7A, CLGN, CLIC2, CLIC3, CLIC4, CLIC5, CLIC6, CLIP1, CLIP2, CLIP4, CLK1, CLK2, CLK3, CLN3, CLN5, CLN6, CLOCK, CLP1, CLPP, CLPTM1, CLPTM1L, CLSTN1, CLSTN2, CLSTN3, CLTA, CLTC, CLTCL1, CLU, CLUH, CLYBL, CMC1, CMC2, CMIP, CMPK1, CMSS1, CMTM2, CMTM3, CMTM4, CMTM5, CMTM6, CMTR1, CMTR2, CMYA5, CNBP, CNFN, CNGA4, CNIH1, CNIH4, CNKSR2, CNKSR3, CNN2, CNN3, CNNM3, CNNM4, CNOT1, CNOT10, CNOT11, CNOT2, CNOT4, CNOT8, CNP, CNPPD1, CNPY3, CNPY4, CNR2, CNRIP1, CNTD1, CNTLN, CNTN1, CNTN5, CNTNAP1, CNTNAP2, CNTROB, COA3, COA4, COA6, COA7, COA8, COASY, COBL, COBLL1, COCH, COG1, COG2, COG4, COG5, COG6, COL11A2, COL15A1, COL17A1, COL18A1, COL19A1, COL1A1, COL26A1, COL4A4, COL5A3, COL6A2, COL8A1, COL9A2, COL9A3, COLCA1, COLEC12, COLGALT1, COLGALT2, COLQ, COMMD1, COMMD10, COMMD2, COMMD6, COMMD9, COMTD1, COP1, COPA, COPB2, COPE, COPG2, COPRS, COPS3, COPS5, COPS7B, COPS9, COPZ1, COQ2, COQ6, COQ7, COQ8A, COQ8B, CORO1A, CORO1B, CORO1C, CORO7, COTL1, COX14, COX17, COX19, COX20, COX5A, COX6A1, COX6B1, COX6C, COX7A1, COX7B, COX7C, COX8A, CP, CPAMD8, CPD, CPE, CPED1, CPLANE1, CPM, CPNE1, CPNE2, CPNE5, CPOX, CPPED1, CPQ, CPSF1, CPSF2, CPSF3, CPSF4, CPSF6, CPT1A, CPT1B, CPTP, CPVL, CR1, CR1L, CR2, CRACR2A, CRADD, CRAMP1, CRAT, CRCP, CRCT1, CREB3, CREB3L1, CREB3L4, CREB5, CREBBP, CREBL2, CREBZF, CREG1, CRELD1, CREM, CRHBP, CRIM1, CRIP1, CRIPT, CRISP3, CRISPLD2, CRK, CRMP1, CRNDE, CRNKL1, CRNN, CROCC, CRTAC1, CRTAM, CRTAP, CRTC1, CRTC2, CRY2, CRYBB1, CRYBG1, CRYBG2, CRYBG3, CRYL1, CRYM, CRYZ, CS, CSAD, CSE1L, CSF2RA, CSF2RB, CSF3R, CSGALNACT1, CSGALNACT2, CSK, CSMD1, CSNK1A1, CSNK1D, CSNK1E, CSNK1G1, CSNK1G2, CSNK1G3, CSPP1, CSRNP1, CSRNP2, CSRNP3, CSRP2, CST3, CSTA, CSTB, CSTF1, CSTF3, CT83, CTBP1, CTBP1-AS, CTBS, CTC1, CTDP1, CTDSP1, CTDSP2, CTIF, CTLA4, CTNNA1, CTNNAL1, CTNNB1, CTNNBIP1, CTNND1, CTPS1, CTPS2, CTR9, CTSA, CTSC, CTSD, CTSF, CTSK, CTSL, CTSS, CTSW, CTSZ, CTTNBP2, CTTNBP2NL, CTU2, CUBN, CUEDC1, CUEDC2, CUL2, CUL3, CUL5, CUL7, CUL9, CUTC, CWC15, CWC22, CWC25, CWC27, CWF19L1, CWF19L2, CX3CR1, CXADR, CXCL1, CXCL10, CXCL11, CXCL12, CXCL16, CXCL17, CXCL2, CXCL3, CXCL6, CXCL9, CXCR1, CXCR3, CXCR4, CXorf38, CXorf40A, CXorf40B, CXorf56, CXXC1, CXXC4, CXXC5, CYB561A3, CYB561D1, CYB561D2, CYB5A, CYB5D2, CYB5R1, CYB5R2, CYB5R3, CYB5R4, CYB5RL, CYBA, CYBB, CYBC1, CYBRD1, CYC1, CYFIP2, CYHR1, CYLD, CYP20A1, CYP27A1, CYP2B6, CYP2E1, CYP2F1, CYP2J2, CYP2R1, CYP2S1, CYP39A1, CYP3A4, CYP3A5, CYP4B1, CYP4F3, CYP4V2, CYP4X1, CYSLTR2, CYSRT1, CYSTM1, CYTH1, CYTH2, CYTH4, CYTIP, CYYR1, CZIB, D2HGDH, DAAM1, DAAM2, DAB1, DAB2, DAB2IP, DAG1, DAGLB, DALRD3, DAPK1, DAPK2, DAPK3, DARS2, DAZAP1, DAZAP2, DBF4B, DBI, DBN1, DBNDD1, DBNL, DBP, DBT, DCAF11, DCAF12, DCAF13, DCAF15, DCAF16, DCAF8, DCAKD, DCBLD1, DCBLD2, DCDC1, DCDC2, DCHS1, DCLK2, DCLRE1B, DCLRE1C, DCP1B, DCSTAMP, DCTN1, DCTN2, DCTN3, DCTN4, DCTN6, DCTPP1, DCUN1D3, DCUN1D4, DCUN1D5, DCXR, DDA1, DDAH1, DDB1, DDB2, DDC, DDHD1, DDI2, DDIAS, DDIT4, DDO, DDOST, DDR1, DDR2, DDRGK1, DDX1, DDX10, DDX11, DDX17, DDX18, DDX19A, DDX19B, DDX21, DDX23, DDX24, DDX27, DDX31, DDX39A, DDX39B, DDX3X, DDX3Y, DDX41, DDX42, DDX47, DDX49, DDX5, DDX51, DDX52, DDX54, DDX55, DDX56, DDX58, DDX59, DDX60, DEAF1, DEF6, DEF8, DEFA1, DEFA1B, DEFA3, DEFB1, DELE1, DENND11, DENND1A, DENND1B, DENND1C, DENND2B, DENND3, DENND4A, DENND4B, DENND4C, DENND5A, DENND6A, DENND6B, DEPDC5, DEPP1, DEPTOR, DERL1, DERL2, DERL3, DESI2, DET1, DEUP1, DEXI, DFFA, DFFB, DGAT1, DGAT2, DGCR2, DGCR6, DGCR8, DGKA, DGKB, DGKD, DGKQ, DGKZ, DGLUCY, DGUOK, DHCR7, DHDH, DHFR, DHODH, DHPS, DHRS1, DHRS12, DHRS13, DHRS3, DHRS4, DHRS7, DHRS9, DHRSX, DHTKD1, DHX15, DHX16, DHX30, DHX32, DHX34, DHX37, DHX38, DHX40, DHX57, DHX9, DIABLO, DIAPH1, DICER1, DIDO1, DIO2, DIP2A, DIP2C, DIPK1A, DIPK1B, DIPK2A, DIS3, DIS3L2, DISP1, DIXDC1, DKC1, DKK1, DLC1, DLD, DLEC1, DLG3, DLG5, DLST, DMAC1, DMAP1, DMBT1, DMD, DMKN, DMPK, DMRT3, DMRTA1, DMTN, DMWD, DMXL1, DMXL2, DNAAF1, DNAH1, DNAH10, DNAH11, DNAH12, DNAH14, DNAH17, DNAH2, DNAH3, DNAH5, DNAH6, DNAH7, DNAH8, DNAH9, DNAH, DNAJA1, DNAJA3, DNAJB11, DNAJB12, DNAJB13, DNAJB14, DNAJB2, DNAJB4, DNAJB6, DNAJB9, DNAJC10, DNAJC14, DNAJC15, DNAJC16, DNAJC17, DNAJC18, DNAJC19, DNAJC21, DNAJC5, DNAJC5B, DNAJC7, DNAJC8, DNAJC9, DNAL1, DNALI1, DNASE1, DNASE1L1, DNASE2B, DNHD1, DNM1, DNM1L, DNM2, DNM3, DNMBP, DNPEP, DNPH1, DNTTIP1, DNTTIP2, DOC2A, DOCK1, DOCK10, DOCK2, DOCK4, DOCK5, DOCK7, DOHH, DOK2, DOK3, DOK6, DOLK, DOT1L, DPEP2, DPF2, DPF3, DPH1, DPH2, DPH3, DPH5, DPH7, DPM1, DPM2, DPM3, DPP3, DPP7, DPP9, DPT, DPY19L3, DPY30, DPYSL2, DPYSL3, DR1, DRAM1, DRAP1, DRC1, DRG2, DROSHA, DSC2, DSC3, DSE, DSG2, DSN1, DSP, DST, DSTN, DSTYK, DTNA, DTNB, DTWD1, DTWD2, DTX1, DTX3, DTX3L, DTX4, DUOX1, DUOX2, DUOXA1, DUOXA2, DUS1L, DUS2, DUS3L, DUSP1, DUSP11, DUSP14, DUSP2, DUSP22, DUSP23, DUSP28, DUSP3, DUSP6, DUSP7, DUSP8, DUXAP9, DVL1, DVL2, DVL3, DXO, DYM, DYNC1H1, DYNC1I2, DYNC1LI2, DYNC2H1, DYNC2LI1, DYNLL1, DYNLL2, DYNLRB1, DYNLRB2, DYNLT1, DYNLT3, DYRK1B, DYRK4, DYSF, DZANK1, DZIP1L, DZIP3, E2F1, E2F2, E2F3, E2F4, E2F7, E4F1, EAF1, EAPP, EARS2, EBAG9, EBF1, EBLN2, EBNA1BP2, EBP, EBPL, ECE1, ECH1, ECHDC2, ECHS1, ECM1, ECPAS, ECRG4, ECSIT, ECT2, ECT2L, EDAR, EDC3, EDC4, EDEM1, EDEM2, EDEM3, EDN1, EDN2, EDNRA, EEA1, EEF1AKMT1, EEF1AKMT3, EEF1B2, EEFID, EEF2, EFCAB1, EFCAB10, EFCAB11, EFCAB14, EFCAB6, EFCAB7, EFEMP1, EFHB, EFHD1, EFHD2, EFL1, EFNA1, EFR3A, EFTUD2, EGF, EGFL6, EGFL7, EGFR, EGLN1, EGLN2, EGOT, EGR1, EGR2, EGR3, EHBP1, EHBP1L1, EHD1, EHD2, EHD3, EHD4, EHF, EHHADH, EHMT1, EHMT2, EID1, EIF1, EIF1AX, EIF1B, EIF2AK1, EIF2AK3, EIF2B2, EIF2B3, EIF2B4, EIF2S1, EIF2S2, EIF2S3, EIF2S3B, EIF3B, EIF3C, EIF3CL, EIF3D, EIF3G, EIF3I, EIF3L, EIF3M, EIF4A1, EIF4B, EIF4E, EIF4E3, EIF4EBP1, EIF4G1, EIF4G2, EIF4H, EIF5A, EIF5AL1, EIF5B, EIF6, EIPR1, ELAC1, ELAC2, ELF2, ELF3, ELF4, ELF5, ELK1, ELK4, ELL, ELL2, ELMO1, ELMO2, ELMO3, ELMOD1, ELMOD2, ELMOD3, ELMSAN1, ELOA, ELOC, ELOVL1, ELOVL5, ELP3, ELP4, ELP5, ELP6, EMB, EMC1, EMC10, EMC2, EMC8, EMC9, EMD, EME2, EMG1, EMID1, EMILIN2, EML1, EML2, EML3, EML4, EML6, EMP2, EMP3, EMSY, ENAH, ENC1, ENDOD1, ENGASE, ENKUR, ENO1, ENO2, ENO3, ENOPH1, ENPP2, ENPP3, ENPP5, ENSA, ENTPD1, ENTPD3, ENTPD4, ENTPD6, EOGT, EP400, EPAS1, EPB41, EPB41L1, EPB41L2, EPB41L3, EPB41L4A, EPB41L4B, EPB41L5, EPB42, EPC2, EPCAM, EPHA1, EPHA2, EPHB6, EPHX2, EPM2AIP1, EPN1, EPN3, EPOR, EPPIN, EPPK1, EPS15, EPS15L1, EPS8, EQTN, ERAL1, ERAP1, ERBB2, ERBB3, ERBB4, ERBIN, ERC1, ERCC1, ERCC2, ERCC3, ERCC5, ERCC6L2, ERCC8, EREG, ERF, ERFE, ERFL, ERG, ERG28, ERGIC1, ERGIC2, ERH, ERI1, ERI2, ERICH1, ERICH3, ERICH5, ERMAP, ERMN, ERN1, ERO1A, ERP29, ERRFI1, ERV3-1, ESCO1, ESD, ESF1, ESPN, ESRP1, ESRP2, ESRRA, ESRRG, ESS2, ESYT1, ESYT2, ETFDH, ETFRF1, ETNK1, ETS1, ETV2, ETV3, ETV5, EVA1B, EVI2A, EVI5, EVI5L, EVL, EWSR1, EXD3, EXOC1, EXOC3, EXOC5, EXOC6B, EXOC7, EXOG, EXOSC1, EXOSC10, EXOSC2, EXOSC4, EXOSC5, EXPH5, EXT2, EXTL3, EYA1, EYA2, EYA3, EYA4, EYS, EZH1, EZH2, EZR, F11R, F12, F13A1, F2R, F2RL1, F2RL2, F2RL3, F3, F5, F8A2, FA2H, FAAH, FAAP100, FAAP20, FABP3, FABP4, FABP5, FABP6, FADS1, FADS2, FADS3, FAF1, FAF2, FAH, FAHD2A, FAHD2B, FAIM, FAM102A, FAM102B, FAM104B, FAM106A, FAM107A, FAM107B, FAM110A, FAM110C, FAM114A1, FAM117A, FAM117B, FAM118A, FAM118B, FAM120A, FAM120AOS, FAM120B, FAM120C, FAM122B, FAM122C, FAM135A, FAM13A, FAM153A, FAM153B, FAM156A, FAM156B, FAM160A1, FAM160A2, FAM160B1, FAM160B2, FAM162A, FAM166B, FAM166C, FAM168A, FAM168B, FAM169A, FAM174A, FAM174C, FAM177A1, FAM183A, FAM184A, FAM185A, FAM186B, FAM189B, FAM193B, FAM199X, FAM200A, FAM204A, FAM209A, FAM20B, FAM210A, FAM210B, FAM214A, FAM214B, FAM216B, FAM217B, FAM219A, FAM219B, FAM220A, FAM222A, FAM222B, FAM229A, FAM229B, FAM234A, FAM3A, FAM3B, FAM3D, FAM47E, FAM49A, FAM50A, FAM53B, FAM53C, FAM71F2, FAM72A, FAM72B, FAM72C, FAM72D, FAM78A, FAM81B, FAM83B, FAM83D, FAM83G, FAM89A, FAM8A1, FAM92A, FAM92B, FAM98C, FANCA, FANCC, FANCD2, FANCI, FANK1, FAP, FAR1, FARP1, FARP2, FASN, FASTK, FASTKD3, FASTKD5, FAT1, FAT3, FAU, FAXDC2, FBH1, FBLN2, FBLN5, FBN2, FBP1, FBRS, FBRSL1, FBXL12, FBXL13, FBXL16, FBXL19, FBXL2, FBXL20, FBXL22, FBXL5, FBXL6, FBXL7, FBXL8, FBX025, FBX028, FBX03, FBXO30, FBXO31, FBXO33, FBXO34, FBXO36, FBXO41, FBXO42, FBXO46, FBXO48, FBXO6, FBXO7, FBXO8, FBXO9, FBXW10, FBXW2, FBXW4, FBXW5, FBXW7, FBXW8, FCAR, FCER1A, FCERIG, FCER2, FCF1, FCGBP, FCGR1A, FCGR1B, FCGR2A, FCGR3A, FCGRT, FCHO1, FCHO2, FCHSD1, FCHSD2, FCMR, FCN1, FCN2, FCRL1, FCRL2, FCRL3, FCRL6, FCRLA, FCSK, FDCSP, FDPS, FDX1, FECH, FEM1A, FEN1, FER, FER1L6, FERMT1, FERMT2, FERMT3, FES, FFAR4, FGD2, FGD3, FGD4, FGD5, FGD6, FGF14, FGF20, FGFBP2, FGFR1, FGFR1OP2, FGFR2, FGFR3, FGGY, FGL2, FGR, FHAD1, FHL1, FHL3, FHOD1, FICD, FILIP1, FILIPIL, FIS1, FIZ1, FKBP11, FKBP15, FKBP1A, FKBP2, FKBP8, FKBPL, FKRP, FLACC1, FLCN, FLG, FLG2, FLU, FLII, FLNA, FLOT2, FLRT3, FLT1, FLT3, FLT3LG, FLT4, FLVCR2, FLYWCH1, FMNL1, FMNL2, FMO2, FMO3, FMO4, FMO5, FMOD, FMR1, FN1, FNBP1L, FNBP4, FNDC10, FNDC3A, FNDC3B, FNIP1, FNIP2, FOCAD, FOLH1, FOLR1, FOLR3, FOPNL, FOS, FOSB, FOSL1, FOSL2, FOXA1, FOXA3, FOXD2-AS1, FOXI2, FOXH, FOXJ2, FOXJ3, FOXK1, FOXK2, FOXM1, FOXN1, FOXN3, FOXO3, FOXO4, FOXP2, FOXP3, FOXQ1, FOXRED1, FPGS, FPGT, FPR1, FPR3, FRA10AC1, FRAT1, FRAT2, FREM2, FRG1, FRK, FRMD4A, FRMD4B, FRMD5, FRMD6, FRMD8, FRMPD3, FRRS1, FRS2, FRY, FRYL, FSCN1, FSD1, FSTL3, FTCDNL1, FTL, FTO, FTSJ1, FUBP1, FUCA1, FUCA2, FUNDC1, FUOM, FURIN, FUS, FUT10, FUT11, FUT2, FUT3, FUT4, FUT7, FUZ, FXR2, FXYD3, FXYD5, FYB2, FYCO1, FYN, FZD1, FZD5, FZD6, FZD7, FZR1, GOS2, G6PC3, G6PD, GAA, GAB2, GABARAP, GABARAPL1, GABBR1, GABPA, GABPB2, GABRB2, GABRP, GABRR2, GADD45B, GADD45G, GAK, GALE, GALK1, GALNS, GALNT1, GALNT10, GALNT12, GALNT2, GALNT5, GALT, GANAB, GAPDH, GAREM1, GAREM2, GARNL3, GART, GAS2L1, GAS2L3, GAS6, GATA1, GATA2, GATA3, GATAD1, GATAD2A, GATD1, GATD3A, GATD3B, GATM, GBA2, GBE1, GBF1, GBGT1, GBP1, GBP3, GBP6, GCA, GCC1, GCC2, GCDH, GCFC2, GCLM, GCN1, GCNA, GCNT2, GCNT3, GCNT7, GCSH, GDA, GDAP1, GDAP2, GDF11, GDF15, GDF9, GDI1, GDPD5, GEMIN4, GEMIN5, GEMIN6, GET1, GET3, GET4, GFI1, GFHB, GFOD1, GFPT1, GFRA2, GGA1, GGA3, GGCX, GGPS1, GGT1, GGT6, GGT7, GHDC, GHITM, GIGYF1, GIMAP4, GIMAP5, GIMAP7, GIN1, GINM1, GINS2, GINS3, GINS4, GIPC3, GIPR, GIT1, GJB3, GJB5, GK, GK5, GKN2, GLB1L2, GLB1L3, GLCE, GLG1, GLI3, GLI4, GLIPR1, GLIS3, GLO1, GLRX, GLRX2, GLRX3, GLRX5, GLT1D1, GLTP, GLUD1, GLUD2, GLUL, GLYATL2, GLYCTK, GLYR1, GM2A, GMDS, GMIP, GMNC, GMNN, GMPPB, GMPR, GMPR2, GNA11, GNA14, GNAI1, GNAI2, GNAI3, GNAL, GNAO1, GNAZ, GNB1, GNB1L, GNB2, GNB4, GNB5, GNG12, GNG2, GNG5, GNG7, GNGT2, GNL1, GNL2, GNLY, GNPDA1, GNPDA2, GNPNAT1, GNPTAB, GNPTG, GOLGA1, GOLGA2, GOLGA3, GOLGA4, GOLGA5, GOLGA6L10, GOLGA7B, GOLGA8A, GOLGA8B, GOLGA8N, GOLGA8R, GOLGB1, GOLIM4, GOLM1, GOLPH3, GOLPH3L, GOLT1B, GORAB, GORASP1, GOSR1, GP1BA, GP5, GP6, GP9, GPAA1, GPALPP1, GPANK1, GPAT2, GPAT3, GPAT4, GPATCH2, GPATCH2L, GPATCH8, GPBAR1, GPBP1, GPBP1L1, GPC2, GPC4, GPCPD1, GPD1, GPD1L, GPD2, GPER1, GPN2, GPN3, GPNMB, GPR107, GPR108, GPR132, GPR137, GPR137B, GPR141, GPR146, GPR153, GPR160, GPR162, GPR171, GPR174, GPR176, GPR183, GPR22, GPR3, GPR34, GPR35, GPR45, GPR55, GPR65, GPR68, GPR75, GPR82, GPR84, GPR85, GPR87, GPR89A, GPR89B, GPRASP2, GPRC5A, GPRIN3, GPS1, GPS2, GPSM1, GPSM3, GPX2, GPX3, GPX8, GRAMD1A, GRAMD1C, GRAMD2A, GRAMD2B, GRAMD4, GRAP, GRAP2, GRAPL, GRASP, GRB10, GRB2, GRB7, GREB1, GRHL1, GRHL2, GRHL3, GRHPR, GRIK2, GRIN2C, GRIN3A, GRINA, GRIP1, GRIPAP1, GRK2, GRK3, GRK5, GRK6, GRM2, GRN, GRWD1, GSDMA, GSDMB, GSDMC, GSDMD, GSE1, GSK3A, GSK3B, GSKIP, GSTA1, GSTA2, GSTA3, GSTA5, GSTCD, GSTK1, GSTM1, GSTM2, GSTM3, GST01, GSTT2, GSTT2B, GSTZ1, GTDC1, GTF2A1, GTF2B, GTF2E1, GTF2F1, GTF2F2, GTF2H1, GTF2H2, GTF2H2C, GTF2H5, GTF2IRD1, GTF3A, GTF3C1, GTF3C2, GTF3C4, GTF3C5, GTF3C6, GTPBP1, GTPBP3, GTPBP6, GTSF1, GUCD1, GUCY1B1, GUCY2C, GUK1, GULP1, GUSB, GXYLT1, GXYLT2, GYPA, GYPB, GYPC, GYS1, GZF1, GZMB, GZMH, GZMK, GZMM, H1-0, H1-1, H1-10, H1-3, H1-4, H1-5, H19, H2AC11, H2AC13, H2AC14, H2AC16, H2AC18, H2AC19, H2AC20, H2AC21, H2AC8, H2AJ, H2AW, H2AZ1, H2AZ2, H2BC12, H2BC18, H2BC7, H3-3A, H3-3B, H3-5, H3C10, H3C12, H3C6, H4C12, H4C13, H4C14, H4C15, H4C2, H4C3, H4C5, H4C9, H6PD, HACD3, HADH, HADHA, HAGH, HAGHL, HAL, HAPLN3, HARB11, HARS1, HARS2, HAT1, HAUS2, HAUS3, HAUS4, HAUS5, HAUS8, HAVCR2, HAX1, HBA1, HBA2, HBB, HBD, HBEGF, HBG1, HBG2, HBM, HBP1, HBQ1, HBS1L, HCAR2, HCFC1, HCFC2, HCK, HCLS1, HDAC1, HDAC10, HDAC11, HDAC3, HDAC4, HDAC5, HDAC6, HDAC7, HDAC8, HDAC9, HDDC2, HDGF, HDGFL2, HDGFL3, HDHD2, HDHD5, HDX, HEATR1, HEATR3, HEATR5A, HEATR6, HECA, HECTD1, HECTD2, HECTD4, HECW2, HELQ, HELZ2, HEMGN, HEMK1, HERC2, HERC4, HERC6, HERPUD1, HERPUD2, HES1, HES2, HESX1, HEXD, HEXIM1, HEXIM2, HEY1, HEY2, HFE, HGH1, HGS, HGSNAT, HHLA2, HIBADH, HIBCH, HIC1, HIC2, HIF1AN, HIGD1A, HIGD2A, HIKESHI, HILPDA, HINT1, HINT3, HIP1R, HIPK1, HIPK2, HIRIP3, HIVEP1, HJURP, HJV, HK1, HK3, HLA-A, HLA-B, HLA-C, HLA-DOB, HLA-DPA1, HLA-DQA2, HLA- DQB2, HLA-E, HLA-F, HLA-G, HLCS, HLF, HLTF, HLX, HM13, HMBOX1, HMBS, HMCES, HMG20B, HMGA1, HMGB1, HMGB2, HMGCR, HMGCS2, HMGN3, HMGN4, HMGN5, HMGXB3, HNF1B, HNMT, HNRNPA0, HNRNPA1, HNRNPA1L2, HNRNPA2B1, HNRNPA3, HNRNPAB, HNRNPC, HNRNPD, HNRNPH1, HNRNPH2, HNRNPH3, HNRNPK, HNRNPL, HNRNPM, HNRNPR, HNRNPU, HNRNPUL1, HOMER1, HOMER2, HOMEZ, HOOK1, HOOK3, HOPX, HOXB2, HOXB3, HOXB6, HPCAL1, HPCAL4, HPGD, HPGDS, HPS1, HPS4, HPS5, HPS6, HPSE, HRH2, HS1BP3, HS2ST1, HS3ST1, HS3ST2, HS3ST3B1, HS6ST1, HSBP1, HSBP1L1, HSD11B1, HSD17B1, HSD17B14, HSD17B4, HSD3B7, HSDL1, HSDL2, HSF1, HSF2, HSF4, HSH2D, HSP90AA1, HSP90AB1, HSPA1A, HSPA1B, HSPA4, HSPA4L, HSPA5, HSPA8, HSPB1, HSPB11, HSPB8, HSPBAP1, HSPBP1, HSPD1, HSPE1, HSPG2, HSPH1, HTATIP2, HTATSF1, HTN1, HTN3, HTRA2, HTRA3, HTRA4, HTT, HUNK, HVCN1, HYDIN, HYKK, HYOU1, HYPK, IAH1, IARS2, IBA57, IBTK, ICAM1, ICAM2, ICAM3, ICAM5, ICE2, ICK, ICMT, ICOSLG, ID1, ID2, ID3, ID4, IDH1, IDH2, IDH3A, IDH3B, IDO1, IDUA, IER2, IER5, IER5L, IFFO1, IFFO2, IFI16, IFI27L2, IFI6, IFIH1, IFITI, IFIT2, IFIT3, IFIT5, IFITM1, IFITM3, IFNG, IFNGR2, IFRD1, IFRD2, IFT22, IFT43, IFT74, IFT81, IGF1, IGF1R, IGF2BP3, IGF2R, IGFBP3, IGFBP5, IGFLR1, IGHMBP2, IGIP, IGLL5, IGSF10, IGSF3, IGSF6, IGSF8, IGSF9B, IK, IKBKB, IKBKE, IKBKG, IKZF1, IKZF2, IKZF3, IKZF5, IL10RA, IL11RA, IL12A, IL12RB1, IL12RB2, IL16, IL17C, IL17RA, IL17RB, IL17RC, IL17RD, IL18, IL18RAP, IL19, IL1A, IL1B, IL1R1, IL1R2, IL1RN, IL20RA, IL20RB, IL21R, IL22RA1, IL24, IL26, IL27RA, IL2RA, IL2RB, IL2RG, IL32, IL33, IL36B, IL36G, IL36RN, IL4I1, IL4R, IL5RA, IL6R, IL7R, ILF2, ILF3, ILK, ILKAP, ILRUN, ILVBL, IMMT, IMPA1, IMPA2, IMPACT, IMPAD1, IMPDH1, INAFM1, INCA1, INF2, ING1, ING2, ING3, ING4, ING5, INHBA, INIP, INKA1, INKA2, INO80, INO80C, INO80D, INO80E, INPP4A, INPP5A, INPP5B, INPP5D, INPP5F, INPP5K, INPPL1, INSL6, INSR, INSYN2A, INTS1, INTS11, INTS12, INTS2, INTS3, INTS5, INTS6, INTS6L, INTS7, INTS8, INTS9, INTU, INVS, IP6K1, IP6K2, IPCEF1, IPO11, IPO13, IPO7, IPO8, IPPK, IQCA1, IQCE, IQCG, IQCH, IQCK, IQCN, IQGAP3, IQSEC1, IQUB, IRAK1, IRAK1BP1, IRAK2, IRAK3, IRF1, IRF2, IRF2BP1, IRF2BP2, IRF2BPL, IRF3, IRF5, IRF6, IRF8, IRF9, IRGQ, IRS1, IRS2, IRX3, ISCA2, ISG15, ISG20, ISG20L2, ISL1, ISOC2, IST1, ISY1, ISYNA1, ITCH, ITGA10, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGAL, ITGAM, ITGAV, ITGAX, ITGB1, ITGB2, ITGB3, ITGB4, ITGB6, ITGB7, ITGB8, ITIH5, ITK, ITM2A, ITM2B, ITM2C, ITPA, ITPKB, ITPR2, ITPR3, ITPRID2, ITPRIP, ITPRIPL1, ITPRIPL2, ITSN1, IWS1, IYD, IZUMO4, JADE1, JADE2, JADE3, JAG1, JAGN1, JAK1, JAK2, JAK3, JAKMIP1, JAKMIP2, JAM3, JAML, JDP2, JHY, JMJD1C, JMJD6, JMJD7-PLA2G4B, JMJD8, JOSD1, JPH4, JPT1, JPT2, JRK, JTB, JUN, JUNB, JUND, KALRN, KANK2, KANSL1-AS1, KANSL1L, KARS1, KAT2A, KAT5, KAT7, KAT8, KATNAL1, KATNAL2, KATNB1, KATNBL1, KAZALD1, KBTBD11, KBTBD2, KBTBD3, KBTBD8, KCNA10, KCNA2, KCNAB1, KCNAB2, KCNAB3, KCNC4, KCND1, KCNE1B, KCNH2, KCNH3, KCNH8, KCNIP2, KCNJ1, KCNJ10, KCNJ13, KCNJ16, KCNJ5, KCNK1, KCNK13, KCNK6, KCNK7, KCNMA1, KCNMB2, KCNN4, KCNQ1, KCNQ3, KCTD1, KCTD11, KCTD12, KCTD13, KCTD17, KCTD20, KCTD7, KCTD9, KDELR1, KDELR2, KDELR3, KDF1, KDM2A, KDM3B, KDM4B, KDM4C, KDM5A, KDM5C, KDM5D, KDM6A, KDM6B, KDM7A, KEL, KHDC4, KHDRBS1, KHDRBS3, KHNYN, KHSRP, KIAA0100, KIAA0232, KIAA0319L, KIAA0355, KIAA0513, KIAA0556, KIAA0586, KIAA0825, KIAA0895, KIAA0895L, KIAA0930, KIAA1143, KIAA1211L, KIAA1217, KIAA1324, KIAA1328, KIAA1522, KIAA1614, KIAA1671, KIAA1841, KIAA1958, KIAA2012, KIAA2013, KIAA2026, KIF16B, KIF20B, KIF21A, KIF21B, KIF22, KIF24, KIF26A, KIF2C, KIF3A, KIF3B, KIF5B, KIFBP, KIFC2, KIN, KIT, KIZ, KLC1, KLC2, KLC3, KLC4, KLF1, KLF10, KLF11, KLF12, KLF13, KLF15, KLF16, KLF2, KLF4, KLF5, KLF6, KLF9, KLHDC2, KLHDC3, KLHDC4, KLHDC8A, KLHDC8B, KLHDC9, KLHL11, KLHL15, KLHL17, KLHL18, KLHL21, KLHL22, KLHL25, KLHL26, KLHL28, KLHL29, KLHL3, KLHL36, KLHL41, KLHL6, KLK1, KLK10, KLK11, KLK13, KLRB1, KLRC2, KLRC3, KLRD1, KLRF1, KLRG1, KLRK1, KMO, KMT2B, KMT2C, KMT2D, KMT2E, KMT5C, KNDC1, KPNA1, KPNA3, KPNA4, KPNA6, KPNA7, KPRP, KPTN, KRBA1, KRBOX4, KRCC1, KRIT1, KRT1, KRT10, KRT13, KRT15, KRT16, KRT17, KRT18, KRT19, KRT23, KRT4, KRT5, KRT6A, KRT6B, KRT6C, KRT7, KRT72, KRT73, KRT78, KRT8, KRT80, KRTCAP2, KSR1, KTI12, KXD1, KYAT3, KYNU, L3MBTL1, L3MBTL2, LACC1, LACTB, LACTB2, LAD1, LAIR2, LAMA1, LAMA2, LAMA3, LAMA5, LAMB1, LAMB2, LAMB3, LAMC1, LAMP3, LAMTOR1, LAMTOR2, LAMTOR3, LAMTOR4, LAMTOR5, LANCL3, LAP3, LAPTM5, LARGE2, LARP1B, LARP4, LARP7, LARS1, LARS2, LAS1L, LASP1, LAT, LAT2, LBH, LBHD1, LBR, LCA5, LCA5L, LCAT, LCE3A, LCE3D, LCE3E, LCK, LCLAT1, LCMT2, LCN2, LCORL, LCP1, LDB1, LDHAL6B, LDHB, LDHD, LDLR, LDLRAD1, LDLRAD2, LDLRAP1, LDOC1, LEF1, LEKR1, LEMD2, LEMD3, LENG8, LEO1, LEP, LEPROT, LEPROTL1, LETM1, LETM2, LETMD1, LFNG, LGALS2, LGALS3, LGALS9B, LGMN, LGR4, LGR6, LHFPL2, LHFPL6, LHPP, LHX4, LIFR, LIG1, LIG3, LIG4, LILRA1, LILRA2, LILRA5, LILRA6, LILRB1, LILRB2, LILRB4, LIMA1, LIMCH1, LIMD1, LIMD2, LIMK1, LIMK2, LIMS1, LIN37, LIN54, LIN7C, LIN9, LINC01410, LINC02701, LINGO3, LIPE, LITAF, LKAAEAR1, LLGL1, LLGL2, LMAN2, LMBR1, LMBR1L, LMCD1, LMF1, LMF2, LMLN, LMNA, LMNTD1, LMNTD2, LMO3, LMO4, LMO7, LMTK2, LMTK3, LNP1, LNX1, LONP1, LONRF2, LOX, LOXHD1, LOXL1, LPAR1, LPAR2, LPAR3, LPAR5, LPCAT1, LPCAT3, LPCAT4, LPGAT1, LPIN2, LPIN3, LPL, LPXN, LRATD1, LRBA, LRCH3, LRCH4, LRFN1, LRFN4, LRG1, LRIF1, LRIG1, LRIG2, LRIG3, LRMDA, LRMP, LRP1, LRP10, LRP11, LRP2BP, LRP3, LRP5L, LRR1, LRRC1, LRRC14, LRRC18, LRRC20, LRRC23, LRRC25, LRRC3, LRRC34, LRRC36, LRRC37A3, LRRC37B, LRRC41, LRRC42, LRRC45, LRRC46, LRRC47, LRRC49, LRRC58, LRRC6, LRRC63, LRRC71, LRRC74A, LRRC8A, LRRCC1, LRRFIP1, LRRIQ1, LRRK1, LRRK2, LRRN1, LRRN2, LRRN3, LRWD1, LSAMP, LSG1, LSM12, LSM14B, LSM3, LSM7, LSP1, LSR, LSS, LTA, LTB, LTB4R, LTB4R2, LTBP1, LTBP3, LTBP4, LTBR, LTK, LTO1, LUC7L, LUC7L2, LUC7L3, LURAP1L, LVRN, LXN, LY6D, LY6E, LY6G5B, LY9, LYL1, LYPD2, LYPD5, LYPD6B, LYPLA2, LYRM2, LYRM4, LYRM9, LYSMD1, LYSMD2, LYSMD3, LYSMD4, LYST, LYVE1, LZTFL1, LZTS2, LZTS3, M1AP, M6PR, MAATS1, MAB21L4, MACC1, MACROH2A1, MACROH2A2, MAD1L1, MAD2L1BP, MAD2L2, MADD, MAEA, MAF1, MAFF, MAFG, MAFK, MAGEE1, MAGEH1, MAGI1, MAGI3, MAGOH, MAGOHB, MAIP1, MAK16, MAL2, MALAT1, MALL, MALSU1, MALT1, MAMDC4, MAML2, MAMLD1, MAN1A1, MAN1B1, MAN2A1, MAN2A2, MAN2B1, MAN2B2, MAN2C1, MANEA, MANEAL, MANF, MANSC4, MAP11, MAP1A, MAP1B, MAP1LC3C, MAP1S, MAP2K2, MAP2K3, MAP2K5, MAP2K6, MAP2K7, MAP3K10, MAP3K11, MAP3K12, MAP3K14, MAP3K19, MAP3K3, MAP3K4, MAP3K6, MAP3K7, MAP4, MAP4K1, MAP4K2, MAP4K3, MAP4K4, MAP4K5, MAP6, MAP7, MAP7D1, MAP9, MAPK10, MAPK11, MAPK14, MAPK1IP1L, MAPK3, MAPK6, MAPK8IP3, MAPKAP1, MAPKAPK3, MAPKBP1, MAPRE1, MARC1, MARCHF1, MARCHF2, MARCHF6, MARCHF8, MARCHF9, MARCO, MARF1, MARK2, MARS1, MARS2, MARVELD1, MARVELD2, MARVELD3, MASP2, MAST3, MASTL, MATK, MAU2, MAVS, MAZ, MB, MBD1, MBD3, MBD4, MBD6, MBLAC1, MBNL1, MBNL2, MBOAT7, MBP, MBTD1, MBTPS1, MC1R, MCC, MCCC1, MCF2, MCFD2, MCIDAS, MCL1, MCM2, MCM3AP, MCM3AP-AS1, MCM4, MCM5, MCM7, MCMBP, MCOLN1, MCPH1, MCR1P1, MCR1P2, MCRS1, MCTP1, MCTP2, MCTS1, MCU, MCUR1, MDGA1, MDH1, MDH1B, MDM2, MDM4, ME1, ME2, ME3, MECOM, MECP2, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED18, MED19, MED21, MED22, MED24, MED25, MED26, MED28, MED30, MED7, MED8, MEF2D, MEFV, MEGF11, MEGF6, MEGF8, MEGF9, MEIS2, MEIS3, MEMO1, MEN1, MEP1A, MEPCE, MEST, MET, METAP1, METAP1D, METAP2, METTL14, METTL17, METTL21A, METTL23, METTL25, METTL3, METTL4, METTL5, METTL6, METTL7B, METTL8, METTL9, MEX3C, MFAP1, MFAP5, MFGE8, MFN2, MFNG, MFSD10, MFSD11, MFSD12, MFSD13A, MFSD14A, MFSD14B, MFSD14C, MFSD2A, MFSD2B, MFSD3, MFSD4A, MFSD4B, MFSD6, MFSD8, MGA, MGAM, MGAT1, MGAT4A, MGAT4B, MGLL, MGRN1, MGST2, MGST3, MIB2, MICAL1, MICAL2, MICAL3, MICALL1, MICALL2, MICOS13, MICU2, MID1, MID1IP1, MIDN, MIEN1, MIER1, MIF4GD, MIGA2, MIIP, MINCR, MINDY2, MINK1, MIPOL1, MIR155HG, MIR421, MIR4435-2HG, MIS12, MITF, MKKS, MKNK2, MKRN1, MLC1, MLEC, MLF1, MLF2, MLH1, MLLT1, MLLT11, MLLT3, MLLT6, MLPH, MLST8, MLX, MLXIP, MLYCD, MMAA, MMAB, MMADHC, MME, MMGT1, MMP1, MMP10, MMP12, MMP17, MMP19, MMP23B, MMP24, MMP25, MMP7, MMP9, MMRN1, MMS19, MMS22L, MMUT, MNAT1, MNS1, MNT, MOAP1, MOB1A, MOB2, MOB3A, MOB3B, MOB3C, MOB4, MOCOS, MOCS2, MOCS3, MOGS, MOK, MORC4, MORN1, MORN2, MORN3, MORN5, MOSPD1, MOSPD2, MOSPD3, MOV10, MPC1, MPC2, MPDU1, MPDZ, MPEG1, MPG, MPHOSPH6, MPIG6B, MPO, MPP1, MPP5, MPPE1, MPRIP, MPST, MPV17, MPV17L, MPV17L2, MPZL2, MR1, MRAP2, MRAS, MRC1, MRFAP1, MRFAP1L1, MRI1, MRM2, MRNIP, MRO, MROH1, MRPL1, MRPL13, MRPL17, MRPL18, MRPL19, MRPL2, MRPL20, MRPL21, MRPL23, MRPL27, MRPL28, MRPL32, MRPL33, MRPL34, MRPL35, MRPL36, MRPL37, MRPL38, MRPL39, MRPL4, MRPL40, MRPL42, MRPL44, MRPL45, MRPL46, MRPL48, MRPL50, MRPL51, MRPL54, MRPL57, MRPL58, MRPS10, MRPS12, MRPS14, MRPS16, MRPS18B, MRPS18C, MRPS2, MRPS23, MRPS25, MRPS26, MRPS30, MRPS31, MRPS33, MRPS34, MRPS35, MRPS36, MRPS5, MRTFA, MRTFB, MS4A1, MS4A14, MS4A2, MS4A3, MS4A4A, MS4A8, MSANTD3, MSANTD4, MSH3, MSH5, MSH6, MSI2, MSL1, MSL2, MSL3, MSLN, MSMB, MSN, MSR1, MSRB1, MSRB3, MSS51, MSTO1, MT1E, MT1F, MT1G, MT1H, MT1X, MT2A, MT3, MTA1, MTA2, MTAP, MT-ATP6, MT-ATP8, MTBP, MTCH1, MTCH2, MT-CO1, MT-CO2, MT-CO3, MT-CYB, MTDH, MTERF1, MTF2, MTFR1L, MTG1, MTHFD1L, MTHFD2, MTHFD2L, MTHFR, MTHFSD, MTIF2, MTIF3, MTLN, MTMR11, MTMR14, MTMR2, MTMR3, MTMR9, MT-ND1, MT-ND2, MT-ND3, MT-ND4, MT-ND4L, MT-ND5, MT-ND6, MTPN, MTR, MTREX, MTRF1, MTRNR2L1, MTRNR2L10, MTRNR2L12, MTRNR2L3, MTRNR2L5, MTRNR2L6, MTRNR2L7, MTRNR2L8, MTRR, MTUS1, MTX1, MTX2, MTX3, MUC1, MUC13, MUC15, MUC16, MUC2, MUC20, MUC21, MUC22, MUC4, MUC5AC, MUC5B, MUC7, MUL1, MUS81, MUTYH, MVB12A, MVD, MVK, MVP, MX1, MXD3, MXD4, MXI1, MXRA7, MXRA8, MYADM, MYB, MYBBP1A, MYBL1, MYBL2, MYCBP2, MYCBPAP, MYCL, MYDGF, MYEF2, MYH14, MYH9, MYL12A, MYL12B, MYL4, MYL5, MYL6, MYL6B, MYL9, MYLIP, MYLK, MYLK4, MYNN, MYO10, MYO15A, MYO15B, MYO18A, MYO19, MYO1B, MYO1C, MYO1D, MYO1E, MYO1F, MYO1G, MYO5A, MYO5B, MYO5C, MYO6, MYO9A, MYO9B, MYOF, MYOM1, MYOM2, MYPOP, MYRF, MYRIP, MYZAP, MZF1, MZT2B, N4BP1, N4BP2L2, N4BP3, N6AMT1, NAA15, NAA16, NAA25, NAA40, NAA50, NAA80, NAAA, NAALADL2, NAB1, NABP1, NACA, NACA2, NACC1, NACC2, NADSYN1, NAGA, NAGK, NAGPA, NAIF1, NAIP, NANP, NAP1L4, NAPA, NAPB, NAPEPLD, NAPRT, NARF, NARS1, NARS2, NAT14, NAT8B, NAT9, NATD1, NAV2, NAXD, NBAS, NBDY, NBEA, NBEAL1, NBEAL2, NBN, NBPF10, NBPF11, NBPF12, NBPF14, NBPF15, NBPF19, NBPF20, NBPF26, NBPF3, NBPF8, NBPF9, NBR1, NCALD, NCAM1, NCAPD2, NCAPD3, NCAPG2, NCAPH2, NCBP2, NCBP3, NCCRP1, NCEH1, NCF1, NCF2, NCK1, NCK2, NCKAP1, NCKAP5, NCKAP5L, NCL, NCLN, NCMAP, NCOA2, NCOA5, NCOA7, NCOR1, NCOR2, NCR1, NCR3, NCS1, NCSTN, NDE1, NDEL1, NDFIP1, NDFIP2, NDN, NDNF, NDOR1, NDRG1, NDRG2, NDST1, NDST2, NDUFA1, NDUFA10, NDUFA12, NDUFA13, NDUFA2, NDUFA3, NDUFA4, NDUFA5, NDUFA6, NDUFA8, NDUFAB1, NDUFAF2, NDUFAF3, NDUFB1, NDUFB2, NDUFB3, NDUFB4, NDUFB6, NDUFB7, NDUFB8, NDUFB9, NDUFC1, NDUFS3, NDUFS4, NDUFS5, NDUFS6, NDUFS7, NDUFV1, NDUFV2, NDUFV3, NEBL, NECAB3, NECAP1, NECTIN4, NEDD9, NEIL1, NEIL3, NEK1, NEK10, NEK11, NEK2, NEK4, NEK5, NEK6, NEK7, NEK8, NEK9, NELFB, NELFCD, NELFE, NEMF, NEMP1, NEMP2, NENF, NEO1, NET1, NETO1, NEU4, NEURL1, NEURL1B, NEURL2, NEURL3, NEURL4, NEXMIF, NF1, NFAM1, NFAT5, NFATC1, NFATC2, NFATC2IP, NFE2, NFE2L1, NFE2L2, NFIA, NFIB, NFIC, NFIL3, NFKB2, NFKBIA, NFKBIB, NFKBID, NFKBIE, NFKBIL1, NFKBIZ, NFS1, NFX1, NFXL1, NFYC, NGEF, NGRN, NHLRC2, NHP2, NHS, NHSL1, NHSL2, NIBAN2, NIBAN3, NIDI, NIF3L1, NIFK, NIN, NINJ2, NINL, NIP7, NIPBL, NISCH, NIT1, NKAP, NKAPD1, NKG7, NKIRAS1, NKIRAS2, NKTR, NKX2-1, NKX3-1, NLGN2, NLGN3, NLK, NLRC3, NLRC4, NLRC5, NLRP1, NLRP12, NLRP3, NLRP6, NLRX1, NMB, NMD3, NME1, NME2, NME3, NME4, NME5, NME7, NME9, NMI, NMNAT2, NMRAL1, NMT1, NMT2, NMUR1, NNAT, NNT, NOC2L, NOC4L, NOCT, NOD2, NOL4L, NOL6, NOL7, NOL9, NOM1, NOMO1, NOMO2, NOMO3, NONO, NOP10, NOP53, NOP56, NOP9, NOS2, NOSIP, NOTCH1, NOTCH2, NOTCH2NLA, NOTCH4, NOX4, NOXA1, NPAS2, NPAS3, NPAT, NPEPL1, NPIPA1, NPIPA2, NPIPA3, NPIPA5, NPIPA7, NPIPA8, NPIPB12, NPIPB13, NPIPB15, NPIPB2, NPIPB3, NPIPB4, NPIPB5, NPIPB6, NPIPB9, NPL, NPLOC4, NPM3, NPNT, NPRL3, NPTN, NPTXR, NPW, NQO1, NR1H2, NR1H3, NR2F2, NR2F6, NR3C1, NR4A1, NR4A2, NRAS, NRBF2, NRBP2, NRCAM, NRDC, NRG1, NRG4, NRGN, NRIP1, NRIP2, NRM, NRP1, NRP2, NRROS, NRXN1, NRXN3, NSA2, NSD1, NSF, NSFL1C, NSG1, NSL1, NSMAF, NSMCE1, NSMCE3, NSMF, NSRP1, NSUN2, NSUN5, NSUN6, NSUN7, NT5C2, NT5DC2, NT5DC3, NT5M, NTAN1, NTF4, NTMT1, NTN4, NTNG2, NTRK3, NTSR1, NUAK1, NUAK2, NUBP1, NUBP2, NUBPL, NUCB1, NUCKS1, NUDCD1, NUDCD2, NUDCD3, NUDT12, NUDT14, NUDT15, NUDT16L1, NUDT17, NUDT19, NUDT2, NUDT21, NUDT22, NUDT3, NUDT5, NUDT8, NUFIP1, NUFIP2, NUGGC, NUMA1, NUP188, NUP205, NUP210, NUP42, NUP50, NUP54, NUP58, NUP62, NUP85, NUP88, NUP93, NUPR1, NUS1, NUTM2A, NUTM2D, NUTM2G, NWD1, NXF1, NXF3, NXN, NXPE3, OAF, OAS1, OAS2, OASL, OAT, OAZ1, OAZ2, OBI1, OBSCN, OCIAD1, OCLN, OCRL, ODF2, ODF2L, ODF3B, OFD1, OGA, OGDH, OGFOD1, OGFOD3, OGFR, OGG1, OGT, OLA1, OLAH, OLFML2A, OLFML2B, OLFML3, OLIG1, OLR1, OMA1, OMD, OMG, OPA3, OPHN1, OPLAH, OPRL1, OR2A4, OR2A42, OR2A7, OR2B6, OR2W3, OR5AU1, ORAI1, ORAI2, ORAI3, ORC1, ORC2, ORC3, ORM2, ORMDL1, ORMDL2, ORMDL3, OS9, OSBP2, OSBPL11, OSBPL1A, OSBPL2, OSBPL5, OSBPL6, OSBPL7, OSBPL8, OSBPL9, OSCP1, OSER1, OSGEP, OSGIN2, OSMR, OSR2, OTOA, OTUB1, OTUB2, OTUD1, OTUD3, OTUD6B, OTUD7B, OTULIN, OTX1, OVCH1, OVGP1, OXA1L, OXER1, OXLD1, OXNAD1, OXSR1, P2RX1, P2RX4, P2RX5, P2RY10, P2RY13, P2RY8, P3H1, P4HA1, P4HA2, P4HB, P4HTM, PABPC1L, PABPC3, PABPN1, PACRG, PACS1, PACS2, PACSIN1, PACSIN2, PADI1, PADI4, PAFAH1B1, PAFAH1B2, PAG1, PAGE2B, PAIP2, PAK1, PAKHP1, PAK4, PALB2, PALLD, PALMD, PAM16, PAN2, PAN3, PANK1, PANK2, PANK4, PANX2, PAPLN, PAPSS1, PAPSS2, PAQR4, PAQR5, PAQR6, PAQR7, PAQR8, PARD3, PARD3B, PARD6A, PARD6B, PARG, PARK7, PARE, PARP1, PARP10, PARP11, PARP14, PARP15, PARP2, PARP4, PARP8, PARVA, PARVB, PARVG, PASK, PATL2, PATZ1, PAX5, PAX9, PAXBP1, PBDC1, PBLD, PBRM1, PBX2, PBX3, PBX4, PBXIP1, PCBD1, PCBP1, PCBP2, PCBP4, PCCA, PCDH12, PCDH9, PCDHGB7, PCED1A, PCED1B, PCGF3, PCGF6, PCIF1, PCLO, PCM1, PCMT1, PCMTD2, PCNA, PCNP, PCNT, PCNX1, PCNX3, PCOLCE2, PCP4L1, PCSK1N, PCSK5, PCSK6, PCSK7, PCYOX1, PCYOX1L, PDAP1, PDC, PDCD1, PDCD10, PDCD11, PDCD1LG2, PDCD2L, PDCD6, PDCL3, PDE2A, PDE3A, PDE4D, PDE4DIP, PDE5A, PDE6B, PDE6D, PDE7A, PDE8A, PDE8B, PDE9A, PDGFA, PDGFC, PDGFRB, PDHA1, PDHX, PDIA3, PDIA4, PDIA5, PDIA6, PDK1, PDK3, PDK4, PDLIM1, PDLIM2, PDLIM3, PDLIM5, PDLIM7, PDP1, PDPR, PDRG1, PDS5B, PDSS1, PDXDC1, PDZD11, PDZD2, PDZD4, PDZD8, PDZK1, PDZK1IP1, PEAK1, PEAK3, PEAR1, PEBP1, PEBP4, PEG10, PEG3, PELI1, PELI2, PELP1, PEMT, PER1, PER2, PER3, PERP, PES1, PET100, PEX1, PEX10, PEX11B, PEX13, PEX16, PEX26, PF4, PF4V1, PFDN1, PFDN2, PFDN5, PFDN6, PFKFB3, PFKFB4, PFKL, PFKM, PFKP, PFN1, PFN2, PFN4, PGA3, PGA4, PGA5, PGAM1, PGAM4, PGAM5, PGAP2, PGAP3, PGAP4, PGAP6, PGBD2, PGBD4, PGD, PGGHG, PGGT1B, PGK1, PGM2, PGM2L1, PGM3, PGM5, PGPEP1, PGRMC1, PGS1, PHACTR1, PHACTR2, PHACTR4, PHAX, PHB2, PHC2, PHC3, PHETA1, PHEX, PHF1, PHF10, PHF12, PHF13, PHF14, PHF19, PHF2, PHF21A, PHF3, PHF5A, PHF6, PHF8, PHKG2, PHLDA1, PHLDA3, PHLDB3, PHLPP1, PHOSPHO1, PHRF1, PHTF2, PHYH, PHYHD1, PHYKPL, PI3, PI4K2A, PI4K2B, PI4KA, PI4KB, PIAS1, PIAS2, PIAS3, PIAS4, PIBF1, PICALM, PICK1, PID1, PIDD1, PIEZO1, PIF1, PIFO, PIGA, PIGF, PIGG, PIGK, PIGL, PIGM, PIGO, PIGP, PIGQ, PIGR, PIGS, PIGT, PIGU, PIGX, PIGZ, PIH1D1, PIH1D2, PIK3C2A, PIK3C2B, PIK3CD, PIK3IP1, PIK3R3, PIK3R5, PIK3R6, PILRB, PIM1, PIM2, PIM3, PIN1, PIN4, PINK1, PIP, PIP4K2A, PIP4K2B, PIP4K2C, PIP4P1, PIP4P2, PIP5K1A, PIP5K1C, PIP5KL1, PIR, PITPNA, PITPNB, PITPNC1, PITPNM1, PITPNM2, PITX1, PIWIL4, PJA2, PKD1, PKD1L3, PKD2, PKD2L1, PKDCC, PKHD1L1, PKIB, PKM, PKMYT1, PKN1, PKNOX1, PKP1, PKP2, PKP3, PKP4, PLA1A, PLA2G10, PLA2G4C, PLA2G6, PLA2G7, PLA2R1, PLAAT2, PLAGL2, PLAT, PLAU, PLAUR, PLBD1, PLCB1, PLCB2, PLCB4, PLCD1, PLCD3, PLCE1, PLCG1, PLCG2, PLCH1, PLCH2, PLCL2, PLCXD1, PLD1, PLD2, PLD3, PLD4, PLD6, PLEC, PLEK, PLEK2, PLEKHA3, PLEKHA5, PLEKHA7, PLEKHF1, PLEKHF2, PLEKHG2, PLEKHG3, PLEKHJ1, PLEKHM1, PLEKHM2, PLEKHM3, PLEKHO2, PLEKHS1, PLGLB1, PLGLB2, PLGRKT, PLIN2, PLIN3, PLIN4, PLK1, PLK2, PLK3, PLOD1, PLOD3, PLP2, PLPP2, PLPP3, PLPP6, PLPPR2, PLS1, PLS3, PLSCR4, PLVAP, PLXDC1, PLXDC2, PLXNA1, PLXNA3, PLXNA4, PLXNB2, PLXNB3, PLXNC1, PLXND1, PMEPA1, PMF1, PMFBP1, PMM1, PMM2, PMP22, PMPCA, PMPCB, PMS1, PMVK, PNISR, PNKD, PNKP, PNMA3, PNMA8A, PNN, PNP, PNPLA1, PNPLA2, PNPLA3, PNPLA4, PNPLA6, PNPLA8, PNPO, POC1B, PODXL, POF1B, POFUT1, POFUT2, POGLUT1, POGLUT3, POLA1, POLA2, POLB, POLDI, POLD3, POLD4, POLDIP2, POLDIP3, POLE, POLE3, POLG, POLG2, POLK, POLL, POLM, POLR1A, POLR1B, POLR2A, POLR2B, POLR2C, POLR2E, POLR2F, POLR2G, POLR2H, POLR2I, POLR2J2, POLR2J3, POLR2K, POLR2L, POLR2M, POLR3B, POLR3C, POLR3E, POLR3F, POLR3H, POLR3K, POLRMT, POM121, POM121C, POMGNT1, POMGNT2, POMK, POMP, POMT1, POMT2, POMZP3, POP4, POPDC2, POR, POSTN, POT1, POTEE, POTEF, POTEI, POTEJ, POU2F1, POU2F2, POU5F2, POU6F1, PP2D1, PPA1, PPA2, PPAN, PPARD, PPARG, PPARGC1A, PPARGC1B, PPBP, PPCDC, PPCS, PPDPF, PPFIA1, PPFIBP1, PPHLN1, PPIB, PPIC, PPID, PPIE, PPIF, PPIG, PPIL1, PPIL2, PPIL4, PPIL6, PPIP5K1, PPL, PPM1A, PPM1B, PPM1D, PPM1F, PPM1G, PPM1H, PPM1K, PPM1L, PPM1M, PPOX, PPP1CA, PPP1CC, PPP1R10, PPP1R12C, PPP1R13L, PPP1R14C, PPP1R15A, PPP1R15B, PPP1R16B, PPP1R18, PPP1R1A, PPP1R1B, PPP1R32, PPP1R36, PPP1R3C, PPP1R3E, PPP1R3F, PPP1R8, PPP1R9A, PPP1R9B, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2D, PPP2R3A, PPP2R5A, PPP2R5B, PPP2R5D, PPP3CA, PPP3CC, PPP3R1, PPP4C, PPP5C, PPP5D1, PPP6C, PPP6R1, PPP6R2, PPP6R3, PPRC1, PPT1, PPT2, PPTC7, PPWD1, PQBP1, PRADC1, PRAF2, PRAG1, PRAM1, PRB1, PRB3, PRB4, PRCC, PRDM1, PRDM10, PRDM15, PRDM2, PRDX1, PRDX2, PRDX3, PREB, PRELID1, PRELID3A, PRELID3B, PREP, PREPL, PREX1, PRF1, PRH2, PRICKLE2, PRICKLE3, PRIMPOL, PRKAAI, PRKAA2, PRKAB1, PRKAB2, PRKACA, PRKACB, PRKAG1, PRKAG2, PRKAG3, PRKAR2A, PRKCA, PRKCB, PRKCD, PRKCH, PRKCI, PRKCQ, PRKCSH, PRKD2, PRKD3, PRKN, PRKRA, PRKRIP1, PRMT1, PRMT2, PRMT6, PRMT7, PRNP, PROCA1, PROCR, PROM1, PROM2, PRORP, PROS1, PROSER3, PROX1, PRPF19, PRPF38B, PRPF39, PRPF40A, PRPF4B, PRPF6, PRPF8, PRPS1, PRPSAP1, PRPSAP2, PRR11, PRR12, PRR13, PRR14, PRR15, PRR15L, PRR18, PRR29, PRR5, PRR7, PRRC1, PRRC2A, PRRC2B, PRRC2C, PRRG3, PRRT4, PRRX1, PRRX2, PRSS12, PRSS16, PRSS21, PRSS23, PRSS3, PRSS36, PRSS53, PRUNE1, PRUNE2, PRX, PRXL2A, PRXL2B, PRXL2C, PSAP, PSCA, PSD, PSD3, PSD4, PSEN2, PSENEN, PSKH1, PSMA2, PSMA3, PSMA4, PSMA6, PSMA7, PSMB1, PSMB10, PSMB2, PSMB5, PSMB7, PSMB8, PSMC2, PSMC3IP, PSMC4, PSMC6, PSMD1, PSMD10, PSMD12, PSMD13, PSMD14, PSMD2, PSMD3, PSMD5, PSMD8, PSME3, PSME4, PSMF1, PSMG1, PSMG2, PSPC1, PSPH, PSRC1, PSTPIP1, PSTPIP2, PTAFR, PTAR1, PTBP1, PTBP2, PTBP3, PTCD1, PTCRA, PTDSS1, PTDSS2, PTER, PTGDR, PTGDS, PTGER2, PTGER3, PTGER4, PTGES, PTGES2, PTGES3L, PTGFR, PTGIR, PTGR1, PTGS1, PTK2, PTK2B, PTMA, PTN, PTOV1, PTP4A1, PTP4A3, PTPA, PTPN12, PTPN13, PTPN14, PTPN18, PTPN23, PTPN3, PTPN4, PTPN6, PTPN7, PTPRC, PTPRE, PTPRF, PTPRJ, PTPRK, PTPRM, PTPRO, PTPRS, PTPRT, PTPRU, PTPRZ1, PTRH2, PTRHD1, PTX3, PUDP, PUF60, PUM2, PUM3, PURA, PURB, PUS1, PUS10, PUS3, PWP1, PWP2, PWWP2B, PWWP3A, PXDC1, PXDN, PXK, PXMP4, PXN, PXYLP1, PYCARD, PYCR2, PYGB, PYGM, PYGO2, PYHIN1, PYM1, PYROXD2, PYURF, QARS1, QPCT, QPCTL, QRICH1, QSER1, QSOX1, QSOX2, QTRT1, R3HDM4, RAB10, RAB11B, RAB11FIP1, RAB11FIP3, RAB11FIP4, RAB12, RAB13, RAB1A, RAB1B, RAB20, RAB21, RAB22A, RAB23, RAB24, RAB25, RAB27A, RAB30, RAB32, RAB35, RAB36, RAB37, RAB38, RAB39A, RAB39B, RAB3C, RAB3D, RAB40B, RAB40C, RAB42, RAB43, RAB44, RAB5IF, RAB6B, RAB7A, RAB7B, RAB8B, RAB9A, RABAC1, RABEP1, RABEP2, RABEPK, RABGAP1, RABGAP1L, RABGEF1, RABGGTA, RABGGTB, RABIF, RABL2A, RABL2B, RABL6, RAC1, RAC2, RAD17, RAD18, RAD23A, RAD51AP1, RAD51D, RAD54L2, RAD9A, RADX, RAE1, RAF1, RAI1, RAI14, RAI2, RALBP1, RALGAPA2, RALGAPB, RALGPS2, RALY, RAMAC, RAN, RANBP10, RANBP17, RANBP2, RANBP6, RANBP9, RANGAP1, RAP1A, RAP1GAP, RAP2A, RAP2B, RAPGEF1, RAPGEF4, RAPH1, RARA, RARB, RARG, RARRES1, RARS1, RARS2, RASA2, RASA3, RASAL2, RASAL3, RASEF, RASGEF1A, RASGEF1B, RASGRP1, RASGRP2, RASGRP3, RASGRP4, RASSF1, RASSF2, RASSF3, RASSF5, RASSF6, RASSF8, RASSF9, RAVER1, RAVER2, RB1, RBBP4, RBBP6, RBBP8, RBBP9, RBCK1, RBFA, RBFOX2, RBL1, RBL2, RBM10, RBM11, RBM12, RBM12B, RBM14, RBM14-RBM4, RBM15, RBM17, RBM18, RBM19, RBM22, RBM23, RBM24, RBM27, RBM3, RBM33, RBM34, RBM38, RBM39, RBM4, RBM41, RBM43, RBM44, RBM47, RBM5, RBM6, RBMS2, RBMS3, RBMX, RBMXL1, RBP1, RBP4, RBP5, RBPJ, RBPMS, RBSN, RBX1, RCBTB2, RCC1, RCC1L, RCE1, RCHY1, RCL1, RCN2, RCN3, RCSD1, RDH10, RDH11, RDH12, RDH13, RDH5, RDX, REC8, REEP3, RELA, RELB, RELCH, RELL2, RELT, REM2, RENBP, REPIN1, REPS1, RER1, RERE, RERG, RESF1, REST, RETREG1, RETREG2, RETREG3, RETSAT, REV3L, REX1BD, REXO1, REXO4, REXO5, RFC1, RFFL, RFK, RFLNB, RFNG, RFTN1, RFWD3, RFX1, RFX2, RFX5, RFX7, RFXANK, RFXAP, RGCC, RGL1, RGL2, RGL3, RGL4, RGN, RGP1, RGPD1, RGPD2, RGPD4, RGPD5, RGPD6, RGPD8, RGS1, RGS12, RGS14, RGS16, RGS17, RGS18, RGS22, RGS3, RGS6, RGS7BP, RGS9, RHAG, RHBDD1, RHBDF2, RHCE, RHCG, RHD, RHEB, RHNO1, RHO, RHOBTB2, RHOBTB3, RHOF, RHOG, RHOQ, RHOT2, RHOU, RHOV, RHOXF2, RHOXF2B, RHPN1, RHPN2, RIBC1, RIBC2, RIC1, RIC8A, RIDA, RIF1, RILP, RILPL2, RIMBP3, RIMBP3B, RIMKLB, RIMS1, RIMS3, RIN1, RIN2, RINL, RIOK1, RIOK2, RIOK3, RIOX1, RIPK1, RIPOR1, RIPOR2, RIPOR3, RMC1, RMDN3, RMND1, RMND5A, RMND5B, RNASE10, RNASE6, RNASE7, RNASEH2C, RNASEK, RNASEL, RNASET2, RND3, RNF10, RNF11, RNF111, RNF121, RNF122, RNF123, RNF125, RNF126, RNF13, RNF139, RNF144A, RNF145, RNF149, RNF150, RNF152, RNF157, RNF165, RNF166, RNF167, RNF169, RNF180, RNF181, RNF182, RNF187, RNF2, RNF20, RNF212, RNF215, RNF217, RNF220, RNF24, RNF25, RNF26, RNF31, RNF38, RNF39, RNF40, RNF41, RNF44, RNF5, RNF6, RNF7, RNF8, RNFT1, RNGTT, RNH1, RNLS, RNPC3, RNPEPL1, RNPS1, RO60, ROBO1, ROBO3, ROCK2, ROGDI, ROMO1, ROPN1B, ROPN1L, RORB, ROS1, RP1, RPA1, RPA3, RPE, RPF1, RPF2, RPGRIP1L, RPL11, RPL12, RPL13A, RPL14, RPL15, RPL17, RPL18A, RPL19, RPL21, RPL22, RPL22L1, RPL23, RPL24, RPL26, RPL26L1, RPL27, RPL27A, RPL28, RPL29, RPL30, RPL31, RPL35, RPL35A, RPL36, RPL36AL, RPL37, RPL37A, RPL38, RPL41, RPL5, RPL6, RPL7, RPL7A, RPL7L1, RPL9, RPLP0, RPLP1, RPLP2, RPN1, RPN2, RPP21, RPP25, RPP25L, RPP30, RPRD1A, RPRD2, RPS11, RPS12, RPS13, RPS14, RPS15, RPS15A, RPS16, RPS17, RPS18, RPS19, RPS20, RPS24, RPS25, RPS27, RPS27A, RPS27L, RPS29, RPS3A, RPS4X, RPS4Y1, RPS5, RPS6, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA4, RPS6KB2, RPS7, RPS8, RPS9, RPSA, RPTN, RPUSD1, RPUSD4, RRAGA, RRAGB, RRAGC, RRAGD, RRAS, RRBP1, RRM1, RRM2B, RRN3, RRP12, RRP8, RRP9, RSAD2, RSBN1, RSF1, RSKR, RSL1D1, RSL24D1, RSPH1, RSPH10B, RSPH10B2, RSPH3, RSPH4A, RSPH9, RSPO3, RSRC1, RSRC2, RSRP1, RTCA, RTEL1, RTF2, RTL5, RTL6, RTL8A, RTL8B, RTL8C, RTN1, RTN3, RTP4, RTTN, RUBCN, RUFY2, RUFY3, RUNDC1, RUNDC3A, RUNX3, RUSC2, RUVBL1, RWDD1, RWDD2B, RWDD4, RXRA, RXRB, RXYLT1, RYK, RYR3, S100A10, S100A11, S100A12, S100A13, S100A14, S100A16, S100A2, S100A3, S100A4, S100A6, S100A7, S100A9, S100B, S100P, S100PBP, SIPR1, S1PR3, S1PR4, S1PR5, SAA1, SAE1, SAFB, SAFB2, SALL4, SAMD1, SAMD10, SAMD12, SAMD14, SAMD15, SAMD3, SAMD4A, SAMD4B, SAMD8, SAMD9, SAMD9L, SAMHD1, SAMM50, SAMSN1, SAP130, SAP18, SAP30, SAP30BP, SAP30-DT, SAPCD2, SAR1B, SARAF, SARS1, SART1, SASH1, SASH3, SAV1, SAXO2, SAYSD1, SBDS, SBF1, SBF2, SBF2-AS1, SBNO1, SBNO2, SCAF1, SCAF11, SCAF4, SCAI, SCAMP2, SCAMP3, SCAMP4, SCAMP5, SCAND1, SCAP, SCARA3, SCARB2, SCARF1, SCCPDH, SCD, SCD5, SCEL, SCFD2, SCGB1A1, SCGB3A1, SCGB3A2, SCIN, SCLY, SCMH1, SCML4, SCN1B, SCN3A, SCNN1A, SCNN1D, SCNN1G, SCO1, SCOC, SCP2, SCPEP1, SCRIB, SCRN2, SCRN3, SCUBE3, SCYL1, SDAD1, SDC2, SDC3, SDCBP, SDCBP2, SDCCAG8, SDE2, SDF4, SDHAF2, SDHB, SDHC, SDHD, SDK1, SDK2, SDR16C5, SDR39U1, SDS, SDSL, SEC11A, SEC14L1, SEC14L2, SEC14L5, SEC14L6, SEC16A, SEC22A, SEC24A, SEC24B, SEC24C, SEC31A, SEC31B, SEC61A1, SEC61A2, SEC61B, SEC61G, SECISBP2, SECISBP2L, SECTM1, SEH1L, SEL1L, SELENBP1, SELENOI, SELENOK, SELENON, SELENOO, SELENOW, SELL, SELP, SELPLG, SEM1, SEMA3A, SEMA3C, SEMA3F, SEMA4A, SEMA4B, SEMA4C, SEMA4D, SEMA4F, SEMA6A, SEMA6B, SEMA6C, SEMA7A, SENP1, SENP3, SENP5, SENP7, SENP8, SEPHS1, SEPHS2, SEPTIN1, SEPTIN10, SEPTIN11, SEPTIN3, SEPTIN4, SEPTIN6, SEPTIN7, SEPTIN9, SERAC1, SERBP1, SERF1B, SERF2, SERGEF, SERHL2, SERINC1, SERINC3, SERINC5, SERPINB1, SERPINB10, SERPINB11, SERPINB12, SERPINB13, SERPINB2, SERPINB3, SERPINB4, SERPINB5, SERPINB9, SERPINE1, SERPINE2, SERPINF1, SERPINF2, SERPING1, SERTAD2, SERTAD3, SERTAD4, SESN2, SESN3, SETD1A, SETD1B, SETD2, SETD4, SETD6, SETD7, SETDB1, SETDB2, SETMAR, SETX, SF1, SF3A1, SF3A2, SF3A3, SF3B1, SF3B2, SF3B3, SF3B4, SF3B6, SFI1, SFMBT2, SFPQ, SFR1, SFRP5, SFSWAP, SFT2D2, SFTPA1, SFTPA2, SFTPB, SFTPC, SFTPD, SFXN1, SFXN5, SGCE, SGK1, SGO2, SGPL1, SGPP2, SGSH, SGSM2, SGSM3, SGTA, SH2B1, SH2B2, SH2B3, SH2D1A, SH2D1B, SH2D2A, SH2D3A, SH2D3C, SH3BGRL, SH3BGRL3, SH3BP1, SH3BP2, SH3BP4, SH3BP5L, SH3D19, SH3GL1, SH3GLB2, SH3KBP1, SH3PXD2A, SH3TC1, SH3TC2, SHARPIN, SHC1, SHC3, SHC4, SHCBP1, SHFL, SHISA2, SHISA5, SHISA6, SHISA7, SHISAL2A, SHKBP1, SHLD3, SHMT1, SHMT2, SHOC1, SHOC2, SHQ1, SHROOM2, SHROOM3, SHTN1, SIAE, SIAH1, SIAH2, SIAH3, SIDT1, SIGIRR, SIGLEC11, SIGLEC12, SIGLEC16, SIGLEC9, SIGMAR1, SIK1, SIK1B, SIK2, SIK3, SIN3B, SIPA1, SIPA1L1, SIPA1L2, SIPA1L3, SIRPA, SIRPB2, SIRPD, SIRT2, SIRT3, SIRT5, SIRT7, SITI, SIVA1, SIX1, SIX2, SIX4, SKA2, SKA3, SKAP1, SKI, SKIL, SKIV2L, SKP1, SLA, SLA2, SLAIN1, SLAIN2, SLAMF8, SLAMF9, SLBP, SLC10A3, SLC10A5, SLC11A1, SLC11A2, SLC12A1, SLC12A4, SLC12A6, SLC12A7, SLC12A9, SLC14A1, SLC15A2, SLC15A3, SLC15A4, SLC16A10, SLC16A13, SLC16A3, SLC16A5, SLC16A6, SLC16A7, SLC16A8, SLC16A9, SLC17A9, SLC18B1, SLC19A1, SLC19A2, SLC19A3, SLC1A1, SLC1A3, SLC1A5, SLC20A1, SLC22A13, SLC22A15, SLC22A17, SLC22A18, SLC22A3, SLC23A1, SLC23A2, SLC24A3, SLC24A4, SLC25A1, SLC25A11, SLC25A14, SLC25A15, SLC25A17, SLC25A20, SLC25A22, SLC25A23, SLC25A24, SLC25A28, SLC25A29, SLC25A3, SLC25A30, SLC25A35, SLC25A36, SLC25A37, SLC25A38, SLC25A39, SLC25A4, SLC25A42, SLC25A43, SLC25A45, SLC25A6, SLC26A1, SLC26A6, SLC26A8, SLC27A1, SLC27A2, SLC27A3, SLC29A1, SLC29A2, SLC29A3, SLC2A1, SLC2A10, SLC2A11, SLC2A12, SLC2A14, SLC2A3, SLC2A4RG, SLC2A6, SLC2A9, SLC30A6, SLC30A7, SLC30A9, SLC31A1, SLC31A2, SLC33A1, SLC34A2, SLC35A2, SLC35A3, SLC35A4, SLC35B2, SLC35B4, SLC35C1, SLC35C2, SLC35D1, SLC35E2A, SLC35E2B, SLC35E4, SLC35F2, SLC35F3, SLC35F6, SLC37A1, SLC37A2, SLC37A3, SLC37A4, SLC38A1, SLC38A10, SLC38A2, SLC38A5, SLC38A6, SLC38A7, SLC38A9, SLC39A1, SLC39A13, SLC39A14, SLC39A3, SLC39A7, SLC3A2, SLC41A2, SLC43A1, SLC43A2, SLC44A1, SLC44A2, SLC44A3, SLC44A4, SLC46A2, SLC47A1, SLC49A3, SLC49A4, SLC4A1, SLC4A11, SLC4A1AP, SLC4A2, SLC4A4, SLC4A7, SLC51A, SLC52A2, SLC52A3, SLC5A4, SLC5A6, SLC5A9, SLC66A1, SLC66A2, SLC66A3, SLC6A12, SLC6A14, SLC6A16, SLC6A20, SLC6A6, SLC6A8, SLC6A9, SLC7A1, SLC7A11, SLC7A2, SLC7A5, SLC7A6, SLC7A7, SLC7A8, SLC8A1, SLC8A3, SLC8B1, SLC9A3R2, SLC9A6, SLC9A7, SLC9A8, SLC9B2, SLC9C2, SLCO2A1, SLCO2B1, SLCO3A1, SLCO4C1, SLF2, SLFN13, SLFN14, SLITRK4, SLITRK6, SLK, SLMAP, SLPI, SLX1A, SLX1B, SLX4, SLX4IP, SMAD3, SMAD5, SMAD9, SMAP2, SMARCA1, SMARCA2, SMARCA4, SMARCA5, SMARCAD1, SMARCB1, SMARCC1, SMARCD1, SMARCD2, SMARCD3, SMC1A, SMC2, SMC6, SMCHD1, SMCR8, SMG1, SMG1P7, SMG5, SMG9, SMIM11A, SMIM11B, SMIM12, SMIM14, SMIM15, SMIM19, SMIM20, SMIM22, SMIM24, SMIM25, SMIM26, SMIM29, SMIM3, SMIM30, SMIM31, SMIM4, SMIM5, SMIM6, SMIM7, SMIM8, SMKR1, SMNDC1, SMOC2, SMOX, SMPD1, SMPD2, SMPD3, SMPD4, SMPDL3A, SMR3B, SMS, SMTN, SMTNL1, SMYD2, SMYD4, SMYD5, SNAI1, SNAI2, SNAP23, SNAP47, SNAPC3, SNAPC4, SNAPC5, SNAPIN, SNCA, SNCAIP, SND1, SNHG1, SNHG16, SNHG3, SNIP1, SNN, SNPH, SNRK, SNRNP200, SNRNP25, SNRNP27, SNRNP35, SNRNP70, SNRPA, SNRPA1, SNRPB, SNRPB2, SNRPD1, SNRPG, SNTB1, SNTN, SNU13, SNUPN, SNW1, SNX1, SNX10, SNX11, SNX13, SNX17, SNX18, SNX19, SNX2, SNX20, SNX22, SNX24, SNX27, SNX30, SNX33, SNX5, SNX6, SNX7, SNX9, SOAT1, SOBP, SOCS3, SOCS5, SOCS6, SOCS7, SOD1, SON, SORBS2, SORBS3, SORCS2, SORD, SORL1, SOS1, SOSTDC1, SOWAHC, SOX12, SOX2, SOX21, SOX5, SOX6, SOX9, SP110, SP2, SPA17, SPACA9, SPAG1, SPAG16, SPAG17, SPAG6, SPAG7, SPAG8, SPAG9, SPARCL1, SPART, SPAST, SPATA17, SPATA18, SPATA2, SPATA20, SPATA2L, SPATA5, SPATC1L, SPATS2, SPATS2L, SPCS3, SPDEF, SPDL1, SPDYE2, SPDYE2B, SPDYE3, SPDYE6, SPECC1L, SPEF1, SPEF2, SPEG, SPEN, SPG21, SPG7, SPHK1, SPHK2, SPI1, SPIB, SPIC, SPIDR, SPIN1, SPIN2A, SPIN2B, SPIN4, SPINDOC, SPINK5, SPINK7, SPINT2, SPIRE1, SPN, SPNS1, SPNS2, SPNS3, SPOCK2, SPON2, SPOP, SPOUT1, SPP1, SPPL2B, SPPL3, SPRED1, SPRED2, SPRR1A, SPRR1B, SPRR2A, SPRR2B, SPRR2D, SPRR2E, SPRR2F, SPRR2G, SPRR3, SPRY4, SPRYD3, SPRYD7, SPSB2, SPTA1, SPTB, SPTBN1, SPTBN2, SPTBN5, SPTLC1, SPTLC3, SQLE, SQOR, SQSTM1, SRA1, SRBD1, SRCAP, SRD5A1, SRD5A2, SRD5A3, SREBF1, SREBF2, SREK1, SREK1IP1, SRF, SRFBP1, SRGAP2, SRGAP2B, SRGAP2C, SRGAP3, SRI, SRM, SRP14, SRP72, SRPRA, SRPRB, SRR, SRRM1, SRRM2, SRRM4, SRRT, SRSF1, SRSF10, SRSF11, SRSF2, SRSF3, SRSF4, SRSF5, SRSF6, SRSF7, SRSF9, SS18L1, SS18L2, SSB, SSBP1, SSBP3, SSBP4, SSH1, SSNA1, SSPN, SSR2, SSR3, SSR4, SSRP1, SSTR2, SSTR3, SSX2IP, STB, STM, ST3GAL1, ST3GAL2, ST3GAL6, ST6GAL1, ST6GALNAC1, ST6GALNAC3, ST6GALNAC4, ST7, STAB1, STAC, STAC3, STAG1, STAG3, STAM, STAM2, STAP1, STAP2, STARD13, STARD3, STARD3NL, STARD4, STARD5, STARD7, STARD9, STAT1, STAT3, STAT4, STAT5A, STAT5B, STAT6, STATH, STAU1, STAU2, STEAP1, STEAP1B, STEAP2, STIL, STIM1, STIMATE, STIMATE- MUSTN1, STING1, STIP1, STK10, STK11, STK11IP, STK16, STK17A, STK17B, STK24, STK25, STK26, STK3, STK32C, STK33, STK35, STK38, STK39, STK4, STK40, STMN1, STMN3, STMND1, STMP1, STN1, STOML1, STON2, STOX1, STOX2, STPG1, STRADA, STRADB, STRAP, STRBP, STRIP1, STRN3, STRN4, STT3A, STT3B, STUB1, STX10, STX12, STX16, STX17, STX18, STX19, STX1A, STX2, STX5, STX6, STX7, STX8, STXBP1, STXBP2, STXBP4, STXBP6, STYX, SUB1, SUCNR1, SUCO, SUDS3, SUFU, SUGP1, SUGP2, SUGT1, SULF1, SULF2, SULT1A2, SULT1A3, SULT1A4, SULT1B1, SULT1C2, SULT2B1, SUMF1, SUMF2, SUMO2, SUN1, SUN2, SUOX, SUPT16H, SUPT5H, SUPV3L1, SURF1, SURF4, SURF6, SUSD3, SUSD6, SUV39H1, SUV39H2, SV2A, SVEP1, SWAP70, SYBU, SYCP2, SYCP3, SYK, SYMPK, SYN1, SYNDIG1, SYNE1, SYNE2, SYNE3, SYNGAP1, SYNGR1, SYNGR2, SYNJ1, SYNJ2BP, SYNM, SYNPO, SYNPO2, SYNRG, SYS1, SYT11, SYT17, SYT6, SYTL1, SYTL2, SYTL3, SYTL5, SYVN1, SZRD1, SZT2, TAB1, TAB2, TACC2, TACC3, TACSTD2, TADA1, TADA2A, TADA3, TAF10, TAF13, TAF15, TAF1C, TAF3, TAF6, TAF6L, TAF8, TAF9, TAF9B, TAGAP, TAGLN2, TAL1, TALDO1, TANC1, TANC2, TANGO2, TANK, TAOK1, TAOK2, TAPI1, TAP2, TAPBP, TAPT1, TARBP2, TARDBP, TARS1, TAS1R3, TAS2RB, TAS2R30, TASOR, TATDN2, TAX1BP1, TAX1BP3, TAZ, TBC1D10B, TBC1D10C, TBC1D14, TBC1D15, TBC1D17, TBC1D22A, TBC1D23, TBC1D24, TBC1D25, TBC1D2B, TBC1D3, TBC1D3C, TBC1D3D, TBC1D3E, TBC1D3H, TBC1D3I, TBC1D3K, TBC1D5, TBC1D8B, TBC1D9B, TBCC, TBCD, TBCE, TBCEL, TBKBP1, TBL1X, TBL3, TBP, TBPL1, TBRG1, TBRG4, TBX1, TBX19, TBX20, TBX21, TBXA2R, TBXAS1, TCAF1, TCAF2, TCAIM, TCEA1, TCEA2, TCEA3, TCEAL1, TCEAL3, TCEAL4, TCEAL8, TCEAL9, TCEANC2, TCF12, TCF25, TCF3, TCF7, TCF7L1, TCF7L2, TCHH, TCHP, TCIRG1, TCL1A, TCTA, TCTE1, TCTEX1D1, TCTN1, TCTN2, TDG, TDP1, TDP2, TDRD3, TDRD6, TDRD7, TDRD9, TEAD1, TEAD3, TECPR1, TECR, TEDC1, TEKT1, TEKT2, TEKT4, TELO2, TENM1, TENM4, TENT2, TENT4A, TENT5A, TENT5C, TEP1, TEPSIN, TERF1, TERF2IP, TES, TESC, TESK1, TESK2, TESMIN, TESPA1, TET1, TET2, TET3, TEXM, TEX26, TEX261, TEX264, TEX9, TFAP2A, TFAP2E, TFAP4, TFB2M, TFCP2L1, TFDP2, TFE3, TFEB, TFEC, TFF1, TFF2, TFF3, TFPI, TFR2, TFRC, TG, TGFB1, TGFB2, TGFB3, TGFBI, TGFBR3, TGFBRAP1, TGM3, TGOLN2, TGS1, THADA, THAP10, THAP5, THAP6, THAP8, THBS1, THEGL, THEMIS, THEMIS2, THOC3, THOC5, THOC6, THOP1, THRA, THRAP3, THRB, THSD1, THTPA, THUMPD3, THYN1, TIAF1, TIAL1, TIAM2, TICAM1, TIFA, TIGD1, TIGD5, TIGD6, TIGIT, TIMM13, TIMM17B, TIMM21, TIMM22, TIMM23, TIMM23B, TIMM44, TIMM50, TIMM8A, TIMM8B, TIMM9, TIMMDC1, TINAGL1, TINF2, TIPARP, TIPRL, TIRAP, TJAP1, TJP1, TKFC, TKT, TKTL1, TLCD2, TLCD3A, TLCD5, TLE1, TLE3, TLE5, TLK2, TLL1, TLN1, TLN2, TLR10, TLR2, TLR3, TLR4, TLR7, TLR8, TM2D2, TM2D3, TM4SF1, TM7SF2, TM7SF3, TM9SF2, TM9SF3, TM9SF4, TMBIM1, TMBIM4, TMBIM6, TMC5, TMC6, TMC8, TMCC1, TMCC2, TMCO1, TMCO3, TMCO5A, TMCO6, TMED1, TMED3, TMED4, TMED6, TMED8, TMED9, TMEM102, TMEM104, TMEM106A, TMEM106B, TMEM106C, TMEM109, TMEM11, TMEM115, TMEM120A, TMEM120B, TMEM121B, TMEM126A, TMEM126B, TMEM127, TMEM129, TMEM131L, TMEM132D, TMEM138, TMEM139, TMEM143, TMEM14A, TMEM14C, TMEM150B, TMEM154, TMEM156, TMEM159, TMEM160, TMEM161A, TMEM161B, TMEM164, TMEM167A, TMEM167B, TMEM168, TMEM170A, TMEM170B, TMEM175, TMEM176B, TMEM179B, TMEM181, TMEM183A, TMEM184B, TMEM184C, TMEM185A, TMEM186, TMEM191C, TMEM199, TMEM201, TMEM204, TMEM205, TMEM208, TMEM209, TMEM212, TMEM214, TMEM216, TMEM217, TMEM222, TMEM223, TMEM229B, TMEM232, TMEM237, TMEM241, TMEM242, TMEM248, TMEM250, TMEM251, TMEM254, TMEM255A, TMEM259, TMEM263, TMEM266, TMEM272, TMEM273, TMEM30B, TMEM33, TMEM38A, TMEM38B, TMEM39B, TMEM40, TMEM41A, TMEM43, TMEM44, TMEM50A, TMEM50B, TMEM51, TMEM52B, TMEM53, TMEM54, TMEM59, TMEM60, TMEM63A, TMEM63B, TMEM67, TMEM68, TMEM69, TMEM71, TMEM79, TMEM80, TMEM86A, TMEM86B, TMEM87A, TMEM87B, TMEM88, TMEM8B, TMEM94, TMEM97, TMIGD2, TMOD1, TMOD3, TMPO, TMPPE, TMPRSS11A, TMPRSS11B, TMPRSS11D, TMPRSS11E, TMPRSS2, TMPRSS4, TMPRSS9, TMSB10, TMSB4X, TMTC2, TMTC3, TMTC4, TMUB1, TMUB2, TMX2, TMX4, TNC, TNFAIP1, TNFAIP2, TNFAIP3, TNFAIP6, TNFAIP8, TNFAIP8L1, TNFAIP8L2, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFRSF11A, TNFRSF12A, TNFRSF13B, TNFRSF13C, TNFRSF14, TNFRSF17, TNFRSF19, TNFRSF1B, TNFRSF21, TNFRSF25, TNFRSF4, TNFRSF8, TNFSF10, TNFSF11, TNFSF12, TNFSF13, TNFSF13B, TNFSF15, TNFSF4, TNFSF8, TNFSF9, TNIP1, TNIP2, TNIP3, TNK2, TNNI2, TNPO1, TNRC18, TNRC6B, TNS3, TNS4, TNXB, TOB1, TOB2, TOGARAM2, TOLLIP, TOM1, TOM1L1, TOM1L2, TOMM20, TOMM34, TOMM40L, TOMM5, TOMM7, TONSL, TOP1MT, TOP3A, TOPORS, TOR1B, TOR2A, TOR3A, TOR4A, TOX2, TOX3, TP53BP1, TP53I13, TP53I3, TP53INP1, TP53RK, TP63, TPCN1, TPCN2, TPD52, TPD52L1, TPD52L2, TPGS1, TPI1, TPM2, TPM4, TPP2, TPPP3, TPR, TPRG1, TPRN, TPSB2, TPST2, TPT1, TRA2A, TRA2B, TRABD, TRABD2A, TRADD, TRAF1, TRAF2, TRAF3IP1, TRAF3IP3, TRAF4, TRAF6, TRAF7, TRAM2, TRANK1, TRAP1, TRAPPC1, TRAPPC10, TRAPPC13, TRAPPC2B, TRAPPC4, TRAPPC5, TRAPPC6B, TRAPPC9, TRAT1, TREM2, TREML1, TREML2, TRERF1, TRGC1, TRHDE, TRIAPI, TRIB1, TRIB2, TRIB3, TRIM10, TRIM11, TRIM13, TRIM14, TRIM16, TRIM2, TRIM21, TRIM23, TRIM24, TRIM28, TRIM29, TRIM32, TRIM33, TRIM35, TRIM36, TRIM39, TRIM41, TRIM44, TRIM46, TRIM47, TRIM5, TRIM52, TRIM56, TRIM58, TRIM6, TRIM62, TRIM65, TRIM66, TRIM68, TRIM69, TRIM71, TRIM8, TRIO, TRIOBP, TRIP10, TRIP11, TRIP13, TRIP6, TRIQK, TRIR, TRMT1, TRMT10C, TRMT11, TRMT1L, TRMT2A, TRMT2B, TRMT5, TRMT6, TRMT61A, TRMT61B, TRMU, TRNAU1AP, TROAP, TRPC4AP, TRPC6, TRPM2, TRPM3, TRPV2, TRPV4, TRUB2, TSACC, TSC1, TSC2, TSC22D2, TSC22D3, TSC22D4, TSEN2, TSEN34, TSEN54, TSFM, TSG101, TSGA10, TSHZ2, TSNARE1, TSNAX, TSPAN1, TSPAN11, TSPAN12, TSPAN14, TSPAN15, TSPAN17, TSPAN18, TSPAN19, TSPAN2, TSPAN3, TSPAN31, TSPAN32, TSPAN33, TSPAN5, TSPAN6, TSPAN8, TSPAN9, TSPO, TSPO2, TSPYL2, TSSC4, TSSK4, TST, TSTA3, TSTD1, TSTD2, TTBK2, TTC1, TTC13, TTC14, TTC16, TTC17, TTC21A, TTC22, TTC23, TTC24, TTC25, TTC26, TTC27, TTC29, TTC3, TTC30A, TTC30B, TTC31, TTC32, TTC34, TTC37, TTC38, TTC39A, TTC5, TTC6, TTC7A, TTC7B, TTC8, TTC9, TTF1, TTI1, TTL, TTLL1, TTLL11, TTLL12, TTLL3, TTLL5, TTLL6, TTLL7, TTN, TTYH1, TTYH2, TTYH3, TUBA1C, TUBA4A, TUBA4B, TUBB, TUBB1, TUBB2A, TUBB4B, TUBB6, TUBE1, TUBG1, TUBGCP2, TUBGCP3, TUBGCP6, TUFM, TULP3, TULP4, TUSC1, TUSC2, TUSC3, TUSC7, TUT7, TWF2, TWISTNB, TWNK, TWSG1, TXK, TXLNB, TXLNG, TXN, TXN2, TXNDC11, TXNDC12, TXNDC15, TXNDC17, TXNDC5, TXNDC9, TXNRD1, TXNRD2, TXNRD3, TYK2, TYMP, TYROBP, TYW1, TYWIB, TYW3, U2AF1, U2AF1L4, U2AF1L5, U2AF2, UACA, UAP1, UAP1L1, UBA1, UBA2, UBA6, UBA7, UBAC2, UBALD1, UBALD2, UBAP1L, UBAP2, UBAP2L, UBASH3A, UBASH3B, UBB, UBC, UBE2C, UBE2D3, UBE2D4, UBE2E1, UBE2F, UBE2G1, UBE2G2, UBE2H, UBE2J2, UBE2L3, UBE2M, UBE2N, UBE2O, UBE2Q1, UBE2Q2, UBE2S, UBE2V1, UBE2V2, UBE2W, UBE2Z, UBE3A, UBE3C, UBE3D, UBE4A, UBFD1, UBIAD1, UBL3, UBL5, UBL7, UBN1, UBP1, UBQLNL, UBR1, UBR3, UBR4, UBR5, UBR7, UBTD1, UBTD2, UBTF, UBXN1, UBXN10, UBXN11, UBXN2B, UBXN6, UBXN7, UBXN8, UCHL1, UCK1, UCKL1, UCP1, UCP2, UEVLD, UFD1, UGDH, UGGT1, UGGT2, UGP2, UGT2A1, UGT2B28, UGT3A2, UHRF1, UHRF1BP1, UHRF1BP1L, UHRF2, ULBP2, ULK1, ULK4, UMAD1, UNC119, UNC119B, UNC13B, UNC13D, UNC45A, UNC50, UNC5CL, UNC93B1, UNK, UNKL, UPB1, UPF1, UPF3A, UPK1B, UPK3B, UPK3BL2, UPP1, UQCC2, UQCR10, UQCR11, UQCRB, UQCRC1, UQCRH, UQCRQ, URB2, URM1, UROD, USF1, USF2, USF3, USO1, USP1, USP11, USP14, USP15, USP19, USP20, USP21, USP22, USP25, USP31, USP32, USP35, USP38, USP39, USP46, USP47, USP48, USP5, USP51, USP53, USP54, USP6NL, USP7, USP9X, UST, UTP14A, UTP15, UTP18, UTP20, UTP25, UTP3, UTP4, UTP6, UTRN, UVSSA, VAC14, VAMP1, VAMP2, VAMP3, VAMP4, VAMP8, VANGL2, VARS1, VARS2, VASP, VAT1, VAV1, VAV2, VCAN, VCL, VCP, VCPIP1, VCPKMT, VDAC1, VDAC2, VEGFA, VEGFB, VENTX, VEPH1, VEZF1, VEZT, VGLL1, VGLL3, VHL, VIL1, VILL, VIPR1, VKORC1, VKORC1L1, VLDLR, VMAC, VMO1, VMP1, VNN1, VNN2, VNN3, VPREB3, VPS13A, VPS13D, VPS16, VPS18, VPS26A, VPS26B, VPS28, VPS29, VPS33B, VPS35, VPS37A, VPS37B, VPS39, VPS41, VPS4A, VPS4B, VPS50, VPS51, VPS52, VPS72, VPS9D1, VRK1, VRK2, VRK3, VSIG1, VSIG10, VSIG10L, VSIG2, VSIR, VSNL1, VSTM1, VSTM2L, VTA1, VTCN1, VTI1A, VWA3A, VWA3B, VWA5A, VWA8, VWF, WAC, WAPL, WAS, WASF1, WASF2, WASHC1, WASHC4, WASHC5, WASL, WBP1, WBP11, WBP2, WBP4, WDCP, WDFY1, WDFY2, WDFY4, WDHD1, WDR1, WDR11, WDR13, WDR18, WDR19, WDR20, WDR24, WDR33, WDR34, WDR36, WDR37, WDR38, WDR4, WDR43, WDR44, WDR45, WDR45B, WDR46, WDR49, WDR5, WDR55, WDR59, WDR6, WDR60, WDR61, WDR62, WDR63, WDR66, WDR7, WDR70, WDR73, WDR74, WDR76, WDR78, WDR81, WDR82, WDR83, WDR830S, WDR86, WDR89, WDR90, WDR91, WDR92, WDR93, WDR97, WDTC1, WDYHV1, WFDC1, WFDC2, WFDC3, WHAMM, WHRN, WIPF2, WIPI1 WIPI2, WIZ, WNK2, WNK3, WNT10B, WNT11, WNT2B, WNT4, WNT5A, WRAP53, WRAP73, WRN, WRNIP1, WSB2, WWC1, WWC2, WWC3, WWP2, WWTR1, XAB2, XAF1, XG, XIAP, XK, XKR6, XKR8, XPA, XPC, XPNPEP1, XPNPEP3, XPO1, XPO4, XPO6, XPO7, XPOT, XRCC3, XRCC4, XRN1, XRN2, XRRA1, XXYLT1, XYLT1, XYLT2, YAE1, YAP1, YARS1, YARS2, YBX3, YEATS4, YES1, YIF1A, YIF1B, YIPF2, YIPF3, YIPF4, YIPF5, YIPF6, YJU2, YKT6, YLPM1, YME1L1, YOD1, YPEL1, YPEL2, YPEL3, YPEL4, YPEL5, YRDC, YTHDC1, YTHDF1, YTHDF2, YTHDF3, YWHAB, YWHAE, YWHAG, YWHAQ, YY1, ZADH2, ZAP70, ZBBX, ZBED3, ZBED4, ZBED5, ZBED6CL, ZBED8, ZBP1, ZBTB1, ZBTB10, ZBTB11, ZBTB16, ZBTB17, ZBTB18, ZBTB2, ZBTB21, ZBTB22, ZBTB24, ZBTB25, ZBTB32, ZBTB34, ZBTB37, ZBTB38, ZBTB39, ZBTB40, ZBTB41, ZBTB43, ZBTB46, ZBTB47, ZBTB48, ZBTB5, ZBTB6, ZBTB7B, ZBTB7C, ZBTB8OS, ZC3H11B, ZC3H12A, ZC3H13, ZC3H14, ZC3H15, ZC3H3, ZC3H4, ZC3H6, ZC3H7B, ZC3HAV1L, ZCCHC10, ZCCHC17, ZCCHC3, ZCCHC7, ZCCHC9, ZCRB1, ZDHHC11, ZDHHC12, ZDHHC16, ZDHHC17, ZDHHC18, ZDHHC20, ZDHHC21, ZDHHC24, ZDHHC5, ZDHHC6, ZDHHC7, ZDHHC8, ZEB2, ZER1, ZFAND1, ZFAND2A, ZFAND2B, ZFAND3, ZFAND5, ZFHX2, ZFHX3, ZFP1, ZFP14, ZFP3, ZFP36, ZFP36L2, ZFP41, ZFP69B, ZFP91, ZFPL1, ZFPM1, ZFR, ZFX, ZFYVE1, ZFYVE16, ZFYVE19, ZFYVE21, ZFYVE26, ZFYVE27, ZFYVE28, ZFYVE9, ZG16B, ZGPAT, ZGRF1, ZHX1, ZKSCAN2, ZKSCAN5, ZKSCAN8, ZMAT1, ZMAT5, ZMIZ1, ZMIZ2, ZMYM3, ZMYM4, ZMYM6, ZMYND10, ZMYND11, ZMYND12, ZMYND19, ZMYND8, ZNF101, ZNF107, ZNF12, ZNF121, ZNF124, ZNF134, ZNF135, ZNF138, ZNF14, ZNF141, ZNF142, ZNF148, ZNF16, ZNF160, ZNF169, ZNF175, ZNF181, ZNF184, ZNF189, ZNF19, ZNF200, ZNF202, ZNF211, ZNF212, ZNF213, ZNF214, ZNF217, ZNF219, ZNF22, ZNF222, ZNF224, ZNF226, ZNF230, ZNF232, ZNF234, ZNF235, ZNF251, ZNF253, ZNF26, ZNF260, ZNF268, ZNF273, ZNF276, ZNF277, ZNF28, ZNF280B, ZNF280D, ZNF281, ZNF282, ZNF283, ZNF285, ZNF287, ZNF296, ZNF3, ZNF300, ZNF302, ZNF316, ZNF317, ZNF318, ZNF319, ZNF324, ZNF324B, ZNF330, ZNF331, ZNF333, ZNF335, ZNF337, ZNF33B, ZNF34, ZNF341, ZNF343, ZNF346, ZNF347, ZNF35, ZNF350, ZNF354B, ZNF354C, ZNF358, ZNF362, ZNF365, ZNF367, ZNF37A, ZNF382, ZNF385A, ZNF394, ZNF395, ZNF407, ZNF408, ZNF41, ZNF414, ZNF418, ZNF419, ZNF420, ZNF426, ZNF428, ZNF429, ZNF43, ZNF430, ZNF431, ZNF436, ZNF438, ZNF439, ZNF440, ZNF441, ZNF442, ZNF444, ZNF445, ZNF449, ZNF451, ZNF454, ZNF462, ZNF467, ZNF468, ZNF469, ZNF470, ZNF471, ZNF473, ZNF474, ZNF48, ZNF480, ZNF484, ZNF486, ZNF493, ZNF500, ZNF501, ZNF510, ZNF512, ZNF512B, ZNF513, ZNF514, ZNF516, ZNF518A, ZNF518B, ZNF524, ZNF525, ZNF527, ZNF528, ZNF532, ZNF540, ZNF547, ZNF548, ZNF552, ZNF554, ZNF555, ZNF557, ZNF561, ZNF562, ZNF564, ZNF566, ZNF569, ZNF570, ZNF572, ZNF576, ZNF579, ZNF580, ZNF585B, ZNF586, ZNF587B, ZNF592, ZNF595, ZNF597, ZNF598, ZNF599, ZNF605, ZNF606, ZNF607, ZNF610, ZNF611, ZNF613, ZNF614, ZNF616, ZNF619, ZNF621, ZNF622, ZNF624, ZNF626, ZNF628, ZNF638, ZNF641, ZNF644, ZNF646, ZNF649, ZNF654, ZNF658, ZNF66, ZNF665, ZNF668, ZNF675, ZNF678, ZNF680, ZNF687, ZNF69, ZNF691, ZNF692, ZNF697, ZNF699, ZNF7, ZNF701, ZNF704, ZNF706, ZNF707, ZNF708, ZNF71, ZNF710, ZNF713, ZNF721, ZNF727, ZNF737, ZNF738, ZNF740, ZNF746, ZNF749, ZNF750, ZNF75D, ZNF76, ZNF761, ZNF764, ZNF765, ZNF766, ZNF768, ZNF770, ZNF771, ZNF774, ZNF780B, ZNF782, ZNF784, ZNF785, ZNF787, ZNF789, ZNF79, ZNF790, ZNF791, ZNF799, ZNF808, ZNF81, ZNF813, ZNF816, ZNF821, ZNF823, ZNF829, ZNF83, ZNF831, ZNF835, ZNF836, ZNF839, ZNF84, ZNF844, ZNF845, ZNF85, ZNF850, ZNF852, ZNF860, ZNF862, ZNF865, ZNF880, ZNF888, ZNF891, ZNF90, ZNF91, ZNF92, ZNF93, ZNHIT3, ZNHIT6, ZP3, ZPR1, ZRANB1, ZSCAN12, ZSCAN2, ZSCAN25, ZSCAN31, ZSCAN9, ZSWIMI, ZSWIM4, ZSWIM7, ZSWIM8, ZSWIM9, ZW10, ZWILCH, ZWINT, ZXDB, ZXDC, ZYX, ZZEF1

TABLE 7A (Gene lists defining myeloid populations increased in 3 compartments derived from co-expression analyses) CoV-2 PBMC Myeloid A1 ADAMDEC1, ADGRE2, AIF1, AOAH, APOBEC3B, APOBR, APOC1, BST1, C1QA, C1QB, C1QC, C1RL, C2, C4A, C4B, C4BPA, C5, C6, CCL18, CCL2, CCL7, CCL8, CD101, CD14, CD163, CD209, CD300C, CD300E, CD300LF, CD33, CD68, CD80, CFD, CFP, CLEC10A, CLEC12A, CLEC12B, CLEC16A, CLEC4A, CLEC4D, CLEC4E, CLEC5A, CLEC6A, CLEC7A, CSF1R, CSF2RA, CSF2RB, CSF3R, CST3, CXCL10, CXCL11, CXCL2, CXCL9, CYBA, CYBB, FCER1G, FCGR1A, FCGR1B, FCGR2A, FCGR2B, FCGR2C, FGR, FLT3, FOLR2, FUT4, GRN, HVCN1, IFI30, IGSF6, IL10RA, IL18, IL1A, IL1RAP, IL1RN, ITGAX, LGALS12, LGALS9, LILRA1, LILRA2, LILRA5, LILRA6, LILRB1, LILRB2, LILRB3, LILRB4, LILRB5, LMNB1, LY86, LYVE1, LYZ, MARCO, MEFV, MERTK, MFGE8, MNDA, MPEG1, MRC1, MS4A4A, MS4A6A, MSR1, NLRP12, NLRP3, NOD2, NTSR1, OSCAR, OTOF, PECAM1, PILRA, PLEK, PRAM1, RNASE3, RNASE6, RNASE7, S100A8, S100A9, SCARB1, SECTM1, SEMA4A, SERPINB9, SERPING1, SIGLEC1, SIGLEC10, SIGLEC5, SIGLEC7, SKAP2, SLC11A1, SLITRK4, SPI1, TGM2, THBD, TLR2, TLR8, TNF, TNFAIP8L2, TNFRSF1B, TNFSF13B, TREM1, TREML4, TYROBP, UNC93B1, VENTX, VSIG4, VSTM1 CoV-2 Lung Myeloid A2 ADAMDEC1, ADGRE1, ADGRE2, AIF1, APOBEC3B, APOBEC3G, APOBR, APOC1, BST1, C1QA, C1QB, C1QC, C2, C4BPA, C4BPB, C6, C8A, CCL18, CCL2, CCL22, CCL7, CCL8, CD14, CD300E, CD33, CD80, CFD, CFP, CHI3L1, CHIT1, CLEC12A, CLEC12B, CLEC1A, CLEC2B, CLEC4A, CLEC4D, CLEC4E, CLEC7A, CSF2, CSF2RB, CSF3R, CST3, CXCL1, CXCL10, CXCL11, CXCL13, CXCL8, CXCR2, CYBA, CYBB, FCER1G, FCGR1A, FCGR2A, FCGR2B, FCGR2C, FCGR3A, FCGR3B, FFAR2, FGR, FOLR2, GRN, IFNL1, IGSF6, IL12B, IL18, IL18RAP, IL1A, IL1B, IL1RAP, IL1RN, IL20, IL23A, IL27, ITGAX, LAMP3, LGALS9, LGALS9C, LILRA5, LILRA6, LILRB1, LILRB2, LILRB3, LILRB4, LILRB5, LMNB1, LY86, LYZ, MNDA, MPEG1, MS4A4A, MS4A6A, MSR1, NLRP3, OLR1, OTOF, PDCD1LG2, PILRA, PLEK, S100A8, S100A9, S1PR5, SECTM1, SEMA4A, SERPINB9, SERPING1, SIGLEC14, SIGLEC5, SLPI, SPI1, TLR2, TNF, TNFSF13B, TNFSF14, TNIP3, TREM1, TREML4, TYROBP, UNC93B1, VSIG4 CoV-2 BAL Myeloid A3 ACE, ADAMDEC1, ADGRE3, AIF1, APOBEC3G, APOC1, C1QA, C1QB, C1QC, C1R, C2, C4BPA, C5, C6, CCL18, CCL2, CCL28, CCL7, CCL8, CD163, CD300LF, CD5L, CD68, CD80, CHI3L1, CLEC2B, CLEC4E, CLEC5A, CLEC6A, CXCL1, CXCL10, CXCL11, CXCL2, CXCL8, CXCL9, CXCR2, FCER1G, FCGR1A, FCGR1B, FCGR2A, FCGR2C, FCGR3A, FCGR3B, FOLR2, IGSF6, IK, IL18, IL1A, IL1B, IL1RN, IL23A, LAMP3, LGALS9B, LGALS9C, LILRB4, LILRB5, LY86, LYVE1, MARCO, MERTK, MNDA, MRC1, MS4A4A, MSR1, OLR1, OTOF, PDCD1LG2, PILRA, RNASE7, SCARB1, SERPING1, SIGLEC1, SIGLEC14, SIGLEC5, SIGLEC7, SKAP2, SLAMF8, SLPI, STAP2, TGM2, TLR8, TNF, TNFAIP8L2, TNFSF13B, TNIP3, TYROBP, VSIG4

TABLE 7B (Overlapping genes in co-expression derived myeloid subpopulations between 3 compartments) PBMC/Lung/BAL ADAMDEC1, AIF1, APOC1, C1QA, C1QB, C1QC, C2, C4BPA, C6, CCL18, CCL2, CCL7, CCL8, CD80, CLEC4E, CXCL10, CXCL11, FCER1G, FCGR1A, FCGR2A, FCGR2C, FOLR2, IGSF6, IL18, IL1A, IL1RN, LILRB4, LILRB5, LY86, MNDA, MS4A4A, MSR1, OTOF, PILRA, SERPING1, SIGLEC5, TNF, TNFSF13B, TYROBP, VSIG4 PBMC/Lung ADGRE2, APOBEC3B, APOBR, BST1, CD14, CD300E, CD33, CFD, CFP, CLEC12A, CLEC12B, CLEC4A, CLEC4D, CLEC7A, CSF2RB, CSF3R, CST3, CYBA, CYBB, FCGR2B, FGR, GRN, IL1RAP, ITGAX, LGALS9, LILRA5, LILRA6, LILRB1, LILRB2, LILRB3, LMNB1, LYZ, MPEG1, MS4A6A, NLRP3, PLEK, S100A8, S100A9, SECTM1, SEMA4A, SERPINB9, SPI1, TLR2, TREM1, TREML4, UNC93B1 PBMC/BAL C5, CD163, CD300LF, CD68, CLEC5A, CLEC6A, CXCL2, CXCL9, FCGR1B, LYVE1, MARCO, MERTK, MRC1, RNASE7, SCARB1, SIGLEC1, SIGLEC7, SKAP2, TGM2, TLR8, TNFAIP8L2 Lung/BAL APOBEC3G, CHI3L1, CLEC2B, CXCL1, CXCL8, CXCR2, FCGR3A, FCGR3B, IL1B, IL23A, LAMP3, LGALS9C, OLR1, PDCD1LG2, SIGLEC14, SLPI, TNIP3 PBMC AOAH, C1RL, C4A, C4B, CD101, CD209, CD300C, CLEC10A, CLEC16A, CSF1R, CSF2RA, FLT3, FUT4, HVCN1, IFI30, IL10RA, LGALS12, LILRA1, LILRA2, MEFV, MFGE8, NLRP12, NOD2, NTSR1, OSCAR, PECAM1, PRAM1, RNASE3, RNASE6, SIGLEC10, SLC11A1, SLITRK4, THBD, TNFRSF1B, VENTX, VSTM1 Lung ADGRE1, C4BPB, C8A, CCL22, CHIT1, CLEC1A, CSF2, CXCL13, FFAR2, IFNL1, IL12B, IL18RAP, IL20, IL27, S1PR5, TNFSF14 BAL ACE, ADGRE3, C1R, CCL28, CD5L, IK, LGALS9B, SLAMF8, STAP2

TABLE 7C (Input genes to trajectory analysis) AASS, ABCD1, ABCD2, ABCD3, ACAA2, ACACB, ACADM, ACADS, ACADVL, ACAT1, ACAT2, ACE, ACO2, ACOX1, ACOX2, ACOX3, ACOXL, ACSL1, ACSL5, ADAM8, ADAMDEC1, ADGRE1, ADGRE2, ADGRE3, ADK, AIF1, AIM2, AK3, AKT2, ALDH4A1, ALDH7A1, ALOX15, AOAH, APOBEC3B, APOBEC3G, APOBR, APOC1, APOL1, APOL2, APOL3, APOL6, ARG1, ART4, ATF3, ATP5A1, ATP5B, ATP5D, ATP5E, ATP5F1, ATP5G1, ATP5G2, ATP5G3, ATP5H, ATP5I, ATP5J, ATP5J2, ATP5L, ATP5O, ATP5S, AUH, BATF2, BATF3, BCL2A1, BCS1L, BDH2, BIRC3, BMX, BST1, BTK, C16orf54, C1QA, C1QB, C1QC, C1R, C1RL, C2, C4A, C4B, C4BPA, C4BPB, C5, C6, C8A, CA2, CASP1, CASP10, CCL13, CCL15, CCL18, CCL19, CCL2, CCL20, CCL22, CCL23, CCL28, CCL5, CCL7, CCL8, CCND2, CCR7, CD101, CD14, CD163, CD180, CD209, CD274, CD300A, CD300C, CD300E, CD300LF, CD33, CD36, CD38, CD4, CD40, CD52, CD5L, CD68, CD72, CD80, CD86, CDKN1A, CEACAM1, CEP89, CERK, CFB, CFD, CFP, CHI3L1, CHI3L2, CHIT1, CLEC10A, CLEC12A, CLEC12B, CLEC16A, CLEC1A, CLEC2B, CLEC4A, CLEC4D, CLEC4E, CLEC4F, CLEC5A, CLEC6A, CLEC7A, CNR2, COA1, COA3, COA4, COA5, COA6, COA7, COX10, COX10-AS1, COX11, COX14, COX15, COX16, COX17, COX18, COX19, COX20, COX4I1, COX4I2, COX5A, COX5B, COX6A1, COX6B1, COX6C, COX7A1, COX7A2, COX7A2L, COX7B, COX7C, COX8A, CPT1A, CPT2, CROT, CS, CSAG3, CSF1R, CSF2, CSF2RA, CSF2RB, CSF3R, CST3, CTSC, CXCL1, CXCL10, CXCL11, CXCL13, CXCL2, CXCL8, CXCL9, CXCR2, CXCR4, CYBA, CYBB, CYC1, CYCS, DECR1, DEF6, DLAT, DLC1, DLD, DLST, DNAJC15, DOCK8, EBI3, ECHDC1, ECHDC2, ECHS1, ECI1, ECI2, EDN1, EGR2, EHHADH, EPB41, ETFA, ETFB, ETFDH, F8, FAS, FCAR, FCER1A, FCER1G, FCER2, FCGR1A, FCGR1B, FCGR2A, FCGR2B, FCGR2C, FCGR3A, FCGR3B, FDCSP, FFAR2, FGL2, FGR, FH, FLT3, FN1, FOLR2, FUT4, FYB1, G6PD, GAD1, GADD45B, GADD45G, GBP1, GBP2, GCDH, GCH1, GCNT1, GIMAP2, GIMAP4, GIMAP5, GLS, GLUD1, GOT1, GPR18, GPR84, GRHPR, GRN, H6PD, HAAO, HACL1, HADH, HADHA, HADHB, HAVCR2, HBG2, HCK, HESX1, HEXB, HHLA2, HIBCH, HLX, HNMT, HRH1, HS3ST1, HS3ST2, HSD11B1, HSD17B4, HVCN1, IDH1, IDH2, IDH3A, IDH3B, IDH3G, IDO1, IER3, IFI27, IFI30, IFI44, IFNL1, IGF1, IGFBP4, IGSF6, IK, IL10RA, IL12A, IL12B, IL15, IL15RA, IL18, IL18R1, IL18RAP, IL1A, IL1B, IL1RAP, IL1RN, IL20, IL23A, IL27, IL2RA, IL2RG, IL31RA, IL4I1, IL6, IL7R, INHBA, IRF1, IRF7, IRS1, IRS2, ITGAM, ITGAX, IVD, JAK2, LAIR1, LAMP3, LAP3, LAT, LCP2, LDHAL6B, LGALS12, LGALS9, LGALS9B, LGALS9C, LILRA1, LILRA2, LILRA5, LILRA6, LILRB1, LILRB2, LILRB3, LILRB4, LILRB5, LIPA, LMNB1, LPAR6, LTA4H, LY75, LY86, LYVE1, LYZ, MAF, MARCO, MCCC2, MDH2, MEFV, MERTK, MFGE8, MNDA, MPC1, MPC2, MPEG1, MRC1, MRPS15, MS4A4A, MS4A6A, MSR1, MT-ATP6, MT-ATP8, MT-CO1, MT-CO2, MT-CO3, MT-CYB, MT-ND1, MT-ND2, MT-ND3, MT-ND4, MT-ND4L, MT-ND5, MT- ND6, NAMPT, NDUFA1, NDUFA10, NDUFA11, NDUFA12, NDUFA13, NDUFA2, NDUFA3, NDUFA4, NDUFA4L2, NDUFA5, NDUFA6, NDUFA8, NDUFA9, NDUFAB1, NDUFAF1, NDUFAF2, NDUFAF3, NDUFAF4, NDUFAF5, NDUFAF6, NDUFAF7, NDUFAF8, NDUFB1, NDUFB10, NDUFB11, NDUFB2, NDUFB3, NDUFB4, NDUFB5, NDUFB6, NDUFB7, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS5, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NDUFV3, NKTR, NLRP12, NLRP3, NOD2, NR3C1, NTSR1, NUBPL, OAS1, OAS2, OAS3, OASL, OAT, OGDH, OLR1, OSCAR, OTOF, OXA1L, OXCT1, P2RY13, P2RY14, PC, PDCD1LG2, PDGFA, PDHA1, PDHB, PDHX, PDK1, PDK2, PDK3, PDK4, PDP1, PDP2, PDPR, PECAM1, PEX13, PEX2, PEX5, PEX7, PFKFB2, PFKFB3, PFKFB4, PFKP, PGD, PHYH, PIK3AP1, PILRA, PKM, PLA1A, PLA2G5, PLEK, POU2F2, PRAM1, PRPS1, PRPS2, PSAT1, PSMA2, PSMB9, PSME2, PSTPIP1, PTCH1, PTPN7, PTX3, PYHIN1, RBKS, RGN, RGS1, RNASE3, RNASE6, RNASE7, RPE, RPIA, S100A8, S100A9, S1PR5, SAMSN1, SCARB1, SCO1, SDHA, SDHAF1, SDHAF2, SDHAF3, SDHAF4, SDHB, SDHC, SDHD, SDS, SECTM1, SELENOP, SEMA4A, SERPINB9, SERPING1, SESN2, SIGLEC1, SIGLEC10, SIGLEC14, SIGLEC5, SIGLEC7, SKAP2, SLAMF7, SLAMF8, SLC11A1, SLC25A17, SLC25A4, SLC27A2, SLC2A1, SLC2A3, SLC2A4, SLC2A5, SLC2A6, SLC31A2, SLC38A6, SLC4A7, SLC7A5, SLCO2B1, SLCO5A1, SLITRK4, SLPI, SOCS1, SP100, SPHK1, SPI1, SRGN, STAP2, STAT1, STAT2, STX11, SUCLA2, SUCLG1, SUCLG2, SURF1, TACO1, TALDO1, TAP1, TAP2, TEK, TGFBI, TGFBR2, TGM2, THBD, THEMIS2, TIMMDC1, TKT, TKTL1, TLR1, TLR2, TLR5, TLR8, TMEM126B, TMEM154, TNF, TNFAIP8L2, TNFRSF11A, TNFRSF1B, TNFSF10, TNFSF13B, TNFSF14, TNFSF4, TNFSF8, TNFSF9, TNIP3, TPST2, TRAP1, TREM1, TREML2, TREML4, TTC19, TYROBP, UBE2L6, ULBP1, ULBP2, UNC93B1, UQCC1, UQCC2, UQCC3, UQCR10, UQCR11, UQCRB, UQCRC1, UQCRC2, UQCRFS1, UQCRH, UQCRHL, UQCRQ, VCAM1, VCAN, VENTX, VSIG4, VSTM1, WARS, XAF1

TABLE 8A (Drugs and compounds targeting IPA upstream regulators via blood, lung, or airway) PBMC-CoV2 vs. PBMC-CTL (Blood) IFNG: Amg 811‡ CSF1: Sunitinib† Anti-IL6: Imiquimod†, PF-04236921‡, Siltuximab†, Sirukumab‡, Sarilumab†, Tocilizumab†, Vobarilizumab‡ Anti-IFNA: AGS-009‡, Rontalizumab‡, Sifalimumab‡, Anifrolumab‡ CD38: Daratumumab†, TAK-079‡ TNKS: XAV-939^(P) TGFB1: SB-431542^(P), SB-525334^(P), EGFR inhibitors: Brigatinib†, Dacomitinib†, Erlotinib†, Gefitinib†, Lapatinib†, Osimertinib†, Vandetanib†, CGP-52411^(P), Afatinib†, AG-490^(P), AG-494^(P), BIBU-1361^(P) BIBX-1382‡, Butein^(P), CP-724714‡, Erbstatin-analog^(P), Lavendustin-a, Lavendustin-c, RG-13022, Tyrphostin, TYRPHOSTIN-1, TYRPHOSTIN-AG-1478^(P), TYRPHOSTIN-AG-18^(P), TYRPHOSTIN-AG-494^(P), TYRPHOSTIN-AG-555, TYRPHOSTIN-AG-82, TYRPHOSTIN- AG-835^(P), WZ-3146^(P), WZ-4002^(P), Neratinib†, AEE788‡, ARRY-334543‡, AST-1306‡, AV- 412‡, AZD8931‡, BMS-599626‡, BMS-690514‡, Canertinib‡, CUDC-101‡, FERb-033^(P), GW-583340^(P), Mubritinib‡, PD-168393^(P), Poziotinib‡, TAK-285‡, Tucatinib‡, Tyrphostin-AG- 825^(P), Tyrphostin-AG-879^(P), XL647‡ ERBB2: EGFR inhibitors INSR inhibitors: Ceritinib†, Dovitinib‡, GSK1838705A^(P), GSK1904529A^(P), Linsitinib‡, NVP- AEW541^(P), NVP-TAE684^(P) BRD4: LY-303511^(P), AT-7519‡, Alvocidib‡, Roscovitine‡ VEGFR inhibitors: Lenvatinib†, Pazopanib†, Sorafenib†, Sunitinib†, ZM-306416^(P) AKT inhibitors: 10-DEBC^(P), A-443644, BML-257, Deguelin, Lonidamine†, Miltefosine†, MK-2206‡ PPARG: Acetyl-farnesyl-cysteine†, T-0070907^(P) PPARA: 2-fluoropalmitic-acid, GW-6471^(P) HIF1A: CAY-10585, YC-1^(P), 1-Benzylimidazole STAT1: Sinensetin IGF1R inhibitors: BMS-536924^(P), BMS-754807‡, Ceritinib†, GSK-1904529A^(P), Linsitinib‡, PQ-401^(P) BAX: BAX-Channel-Blocker Drugs Predicted As Upstream Regulators (Inhibited): GnRH analog, Levodopa†, MEL S3, Calcitriol†, CD 437, Ciprofloxacin†, ST1926, 5-fluorouracil†, Sirolimus†, Medroxyprogesterone acetate†, Valproic acid†, BMS-690514‡, Panobinostat†, BMS-754807‡ Lung-CoV2 vs. Lung-CTL (Lung) NFxB pathway inhibitors: CAY-10470^(P), Quinacrine†, Quinoclamine, Auranofin†, BAY-11- 7082^(P), BAY-11-7085^(P), Betulinic-acid‡, Bicyclol†, Bindarit‡, Bortezomib†, Cepharanthine‡, CKD-712‡, Closantel†, Curcumin†, Edasalonexent†, Erythromycin†, EVP4593^(P), E3330^(P), Ginsenoside-C-K‡, Hexamethylenebisacetamide‡, Iguratimod†, IKK-2-inhibitor-V‡, MD- 920‡, NFKB-activation-inhibitor-II^(P), Parthenolide‡, Parthenolide-(-)^(P), Parthenolide- (alternate-stereo)^(P), Pyrrolidine-dithiocarbamate^(P), Ro-106-9920^(P), Sasapyrine†, Sesamin^(P), SP- 100030^(P), Ursolic-acid‡, Verbascoside‡ IL12: Ustekinumab† Lymphotoxin: Etanercept† IFNG: Amg 811‡ Anti-IL17: Brodalumab†, Ixekizumab†, Secukinumab† Anti-TNF: Etanercept†, Adalimumab†, Certolizumab pegol†, Golimumab†, Infliximab† Anti-IFNA: AGS-009‡, Rontalizumab‡, Sifalimumab‡, Anifrolumab‡ Anti-IL1: Canakinumab†, Anakinra† IFNB1: PF-06823859‡ TNFSF12: BIIB023‡ TGM2: GK921^(P), LDN-27219^(P) RNASE1: Citric acid^(P), Guanidine†, L-aspartic-acid† APC: JW-67^(P) NOS2: AR-C133057XX, Diphenyleneiodonium^(P), Pyrrolidine-dithiocarbamate^(P) ETV6-NTRK3: Entrectinib†, GNF-5837^(P), Larotrectinib† Interferon: Anti-IFNA, Amg 811†, Anti-IFN OMEGA‡, PF-06823859‡ JAK inhibitors: AT-9283‡, Baricitinib†, Cucurbitacin-I, Filgotinib‡, Ruxolitinib†, Solcitinib‡, Tofacitinib†, Upadacitinib†, AG-490^(P), Atiprimod, Atractylenolide-i^(P), AZD1480‡, AZ960^(P), BMS-911543‡, CEP-33779^(P), Curcumol‡, cyt387‡, Decernotinib‡, Delgocitinib‡, Fedratinib†, Ganoderic-acid-a^(P), Itacitinib‡, JAK3-inhibitor-V^(P), LY2784544‡, NS-018‡, NVP-BSK805^(P), Pacritinib‡, Peficitinib†, PF-06651600‡, Ruxolitinib-(S)^(P), TCS-21311^(P), TG-02‡, TG- 101209^(P), Thiram†, WHI-P154^(P), XL019‡, ZM-39923^(P), 1,2,3,4,5,6-hexabromocyclohexane^(P) Tlr: Hydroxychloroquine† Tnf (family) inhibitors: Anti-TNF, Dapirolizumab pegol‡, BIIB023t, Atacicept‡, RC18‡, Amg 570‡, Belimumab†, Blisibimod‡, Tabalumab‡ Drugs Predicted As Upstream Regulators (Inhibited): Alefacept, Etanercept†, Fontolizumab, Leuprolide†, Hydrogen peroxide, AT^(P), Hydroquinone†, Nitric oxide, Estriol†, Norepinephrine†, D-glucose, Sphingosine-1-phosphate, Dexamethasone†, Methylprednisolone†, Raloxifene†, 3-deazaneplanocin^(P), Dalfampridine†, Medroxyprogesterone acetate†. Lithium chloride, Chloropromazine, Tofacitinib†, Nelfinavir†, Chloroquine†, Quercetin† BAL-CoV2 vs. PBMC-CoV2 (Airway) Anti-IL17: Brodalumab†, Ixekizumab†, Secukinumab† CD3: Blinatumomab† FCER1: Omalizumab PXR-ligand-PXR-Retinoic acid-RXRα: Retinol†, Fenretinide† IL13: Lebrikizumab† IL2: Daclizumab† FLT3LG: Midostaurin†, Quizartinib‡, Sorafenib†, TCS-359^(P) IL3: Talacotuzumab† LIPE: Oxybenzonet†, Benzyl-benzoate† B4GALNT1: Dinutuximab† SIRT3: Tenovin-6^(P) RNASE1: Citric acid^(P), Guanidine†, L-aspartic-acid† EWSR1-FLI1: YK-4-279^(P) Nr1h: GW-4064^(P) Anti-Hsp90: Alvespimycin‡, BIIB021‡, Gedunin^(P), Geldanamycin^(P), NVP-AUY922‡, PU- H71‡, Radicicol, Tanespimycin‡ IL12: Ustekinumab† JAK inhibitors: AT-9283‡, Baricitinib†, Cucurbitacin-I, Filgotinib‡, Ruxolitinib†, Solcitinib‡, Tofacitinib†, Upadacitinib†, AG-490^(P), Atiprimod‡, Atractylenolide-i^(P), AZD1480‡, AZ960^(P), BMS-911543‡, CEP-33779^(P), Curcumol‡, cyt387‡, Decernotinib‡, Delgocitinib‡, Fedratinib†, Ganoderic-acid-a^(P), Itacitinib‡, JAK3-inhibitor-V^(P), LY2784544‡, NS-018‡, NVP-BSK805^(P), Pacritinib, Peficitinib‡, PF-06651600‡, Ruxolitinib-(S)^(P), TCS-21311^(P), TG-02‡, TG- 101209^(P), Thiram†, WHI-P154^(P), XL019t, ZM-39923^(P), 1,2,3,4,5,6-hexabromocyclohexane^(P) PRKCQ: Afimoxifene‡, Dexfosfoserine^(P), GSK690693‡, Sotrastaurin‡, Tamoxifen† LCK: Aminogenistein, JW-7-24-1, PP-2^(P), WH-4023 ROCK inhibitors: Fasudil†, Ripasudil†, GSK-429286A^(P), GSK-269962^(P), KD025‡, LX7101‡, OXA-06^(P), RKI-1447^(P), SB-772077B^(P), SR-3677^(P), Y-39983†, Y-27632^(P) Estrogen receptor antagonists: Tamoxifen†, Acolbifene‡, Afimoxifene‡, Clomifene†, Danazol†, Endoxifen‡, Fulvestrant†, G-15^(P), GDC-0927‡, PHTPP^(P), Raloxifene†, Toremifene†, Y-134^(P), ZK-164015^(P) AR: Androstenedione, BMS-641988, Enzalutamide†, Flutamide†, Nilutamide† SNH: SANT-1^(P), SANT-2^(P) STATE Sinensetin EPAS1: Cephaeline, YC-1^(P), TC-S-7009^(P), PT-2385‡ GATA3: Cyclosporin-a†, Simvastatin†, Tacrolimus† TEAD2: Oleoylethanolamide^(P) IKZF3: Lenalidomide† ATF2: Ephedrine-(racemic)† ITGB2: BMS-587101‡, Simvastatin† TLR3: CU-CPT-4a^(P) Anti-IL6: Imiquimod†, PF-04236921‡, Siltuximab†, Sirukumab‡, Sarilumab†, Tocilizumab†, Vobarilizumab‡ Drugs Predicted As Upstream Regulators (Inhibited): 15-deoxy-delta-12, 14-PGJ 2, Hydrocortisone†, SB203580, JAK inhibitor I, UM101, Z-DEVD-FMK, Triptolide‡, Etretinate{circumflex over ( )} Legend: †FDA-approved; ‡Drug in development/clinical trials; ^(P)Preclinical; {circumflex over ( )}Withdrawn from market

TABLE 8B (Unique IPA-predicted drugs by mechanism of action in blood, lung, or airway) PBMC (blood) Abl kinase inhibitor, ACE inhibitor, activator of soluble guanylyl cyclase, ALK tyrosine kinase receptor mutant inhibitor, Anti-CD38, Anti-IFNAR1, Anti-IFNG, Anti-IL6, Anti-IL6 receptor, Anti-TNF, apoptosis stimulant, bacterial DNA gyrase inhibitor, Benzodiazepine receptor agonist, CCR expression inhibitor, cell cycle inhibitor, COX inhibitor, CSFR antagonist, cytochrome C release inhibitor, dopamine precursor, ErbB2 tyrosine kinase inhibitor, FGFR inhibitor, glucokinase inhibitor, GnRH agonist, hypercalcaemic agent, hypoxia inducible factor inhibitor, IFNA inhibitor, inhibitor of methylation of endogenous isoprenylated proteins, insulin growth factor receptor inhibitor, insulin receptor ligand, interferon inducer, interleukin inhibitor, kinase inhibitor, KIT inhibitor, Leucine rich repeat kinase inhibitor, MCL1 inhibitor, membrane integrity inhibitor, NADH-ubiquinone oxidoreductase (Complex I) inhibitor, NFκB pathway inhibitor, PDGFR inhibitor, phorbol ester-induced ornithine decarboxylase (ODC) activity suppressor, PPAR receptor antagonist, Proteasome inhibitor, RAF inhibitor, receptor tyrosine protein kinase inhibitor, RET tyrosine kinase inhibitor, SIRT activator, Src inhibitor, Src tyrosine kinase inhibitor, steroid 5alpha- reductase inhibitor, survivin inhibitor, T cell inhibitor, TGF beta receptor inhibitor, thromboxane synthase inhibitor, thymidylate synthase inhibitor, TLR agonist, TNKS inhibitor, tyrosine kinase inhibitor, VEGFR inhibitor, vitamin D receptor agonist, XIAP inhibitor Lung Abl kinase inhibitor, acetylcholinesterase inhibitor, adiponectin receptor agonist, adrenergic receptor agonist, aldehyde dehydrogenase inhibitor, aldose reductase inhibitor, algicide, ALK expression enhancer, Anti-CD2, Anti-CD40LG, Anti-ICOSLG, Anti-IFNAR1, Anti-IFNB1, Anti-IFNG, Anti-IFNW1, Anti-IL1, Anti-IL17, Anti-IL17 receptor, antimalarial agent, Anti- TNF, Anti-TNFSF12, Anti-TNFSF13, Anti-TNFSF13B, AP inhibitor, apoptosis stimulant, Bcr-Abl kinase inhibitor, CCN expression inhibitor, chitinase inhibitor, cholesterol inhibitor, coagulation factor inhibitor, corticosteroid agonist, COX inhibitor, cytochrome P450 inhibitor, cytokine production inhibitor, diacylglycerol O acyltransferase inhibitor, differentiation inducer, disease modifying antirheumatic drug, DNA inhibitor, DNA methyltransferase inhibitor, endoglin expression enhancer, ErbB2 tyrosine kinase inhibitor, Estrogen receptor agonist, free radical scavenger, FtsZ inhibitor, glucocorticoid receptor modulator, glucose 6 phosphatase inhibitor, glucosidase inhibitor, GnRH agonist, growth factor receptor inhibitor, histone lysine methyltransferase inhibitor, histone N-acetyltransferase inhibitor, HIV integrase inhibitor, HIV protease inhibitor, IFNA inhibitor, IL12/23 inhibitor, immunosuppressant, lipocortin synthesis stimulant, lipoxygenase inhibitor, MAPK inhibitor, melanin inhibitor, metallic radical formation stimulant, mitotic inhibitor, monoamine oxidase inhibitor, NADPH oxidase inhibitor, NFκB pathway activator, NFκB pathway inhibitor, nitric oxide synthase inhibitor, phospholipase inhibitor, polar auxin transport inhibitor, potassium channel blocker, prostanoid receptor antagonist, Proteasome inhibitor, proto-oncogene tyrosine protein kinase inhibitor, quorum sensing signaling modulator, SARS coronavirus 3C-like protease inhibitor, selective estrogen receptor modulator, SIRT activator, sodium channel blocker, STAT inhibitor, steroidal receptor agonist, tau aggregation inhibitor, thioredoxin reductase inhibitor, tissue transglutaminase inhibitor, TP53 activator, transglutaminase inhibitor, tropomyosin receptor kinase inhibitor, tyrosine kinase inhibitor, WNT pathway inhibitor, xanthine oxidase inhibitor BAL (airway) Abl kinase inhibitor, activator of soluble guanylyl cyclase, adrenergic receptor agonist, ALK expression enhancer, Anti-B4GALNT1, Anti-CD19, Anti-CD3, Anti-FCER1A, Anti-IL13, Anti-IL17, Anti-IL17 receptor, Anti-IL2R, Anti-IL3R, Anti-IL6, Anti-IL6 receptor, Anti- MS4A2, Anti-TNF, apoptosis stimulant, AR antagonist, ATP citrase lyase inhibitor, Bcr-Abl kinase inhibitor, binding of RNA helicase A to the transcription factor EWS-FLI1 inhibitor, calcium channel activator, calcium sensitizer, cell cycle inhibitor, cereblon inhibitor, cholesterol inhibitor, coagulation factor inhibitor, colony stimulating factor, corticosteroid agonist, COX inhibitor, cyclin inhibitor, cyclophilin inhibitor, cytochrome P450 inhibitor, disease modifying antirheumatic drug, DNA directed DNA polymerase inhibitor, endoglin expression enhancer, ErbB2 tyrosine kinase inhibitor, Estrogen receptor agonist, estrogen receptor modulator, EWS-FLI1 inhibitor, FK506-binding protein inhibitor, FXR agonist, glucose-dependent insulinotropic receptor agonist, histamine release inhibitor, hypoxia inducible factor inhibitor, IL12/23 inhibitor, immunostimulant, immunosuppressant, insulin expression inhibitor, integrin antagonist, interferon inducer, interleukin inhibitor, kinase inhibitor, KIT inhibitor, LCK inhibitor, Leucine rich repeat kinase inhibitor, LIM kinase inhibitor, lipase inhibitor, lipocortin synthesis stimulant, luteinizing hormone releasing hormone antagonist, macrolide calcineurin inhibitor, MAPK inhibitor, membrane integrity inhibitor, metallic radical formation stimulant, mitotic inhibitor, multi targeted kinase inhibitor, opioid receptor ligand, PKA inhibitor, potassium channel blocker, PPAR receptor agonist, PPAR receptor antagonist, protease inhibitor, pyruvate dehydrogenase kinase inhibitor, RAF inhibitor, RET tyrosine kinase inhibitor, retinoid receptor agonist, RNA directed RNA polymerase inhibitor, ROCK inhibitor, rotamase inhibitor, selective estrogen receptor modulator, SIRT inhibitor, soluble epoxide hydrolase inhibitor, Src inhibitor, STAT inhibitor, steroid derivative with antigonadotropic and anti-estrogenic activities, stress activated protein kinase inhibitor, T cell inhibitor, testosterone receptor agonist, TLR agonist, TLR inhibitor, TNF modulator, tumor apoptosis inducer, tyrosine kinase inhibitor, VEGFR inhibitor Legend: † FDA-approved; ‡ Drug in development/clinical trials; ^(P) Preclinical; {circumflex over ( )} Withdrawn from market

Further details are described by, for example, Daamen et al., “Comprehensive transcriptomic analysis of COVID-19 blood, lung, and airway”, Scientific Reports, Vol. 11, No. 7052 (2021), which is incorporated by reference herein in its entirety.

While preferred embodiments have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the scope of the disclosure. It should be understood that various alternatives to the embodiments described herein may be employed in practice. Numerous different combinations of embodiments described herein are possible, and such combinations are considered part of the present disclosure. In addition, all features discussed in connection with any one embodiment herein can be readily adapted for use in other embodiments herein. It is intended that the following claims define the scope of the disclosure and that methods and structures within the scope of these claims and their equivalents be covered thereby. 

What is claimed is:
 1. A method for determining a COVID-19 disease state of a subject, comprising: (a) assaying a biological sample obtained or derived from the subject to produce a data set comprising gene expression measurements of the biological sample at each of a plurality of COVID-19 disease-associated genomic loci, wherein the plurality of COVID-19 disease-associated genomic loci comprises at least a portion of a gene selected from the group of genes listed in Table 6 and Tables 7A-7C; (b) computer processing the data set to determine the COVID-19 disease state of the subject; and (c) electronically outputting a report indicative of the COVID-19 disease state of the subject.
 2. The method of claim 1, wherein the plurality of COVID-19 disease-associated genomic loci comprises at least a portion of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000, 5100, 5200, 5300, 5400, 5500, 5600, 5700, 5800, 5900, or 6000 genes selected from the group of genes listed in Table 6 and Tables 7A-7C.
 3. The method of claim 1, further comprising determining the COVID-19 disease state of the subject with an accuracy of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 4. The method of claim 1, further comprising determining the COVID-19 disease state of the subject with a sensitivity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 5. The method of claim 1, further comprising determining the COVID-19 disease state of the subject with a specificity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 6. The method of claim 1, further comprising determining the COVID-19 disease state of the subject with a positive predictive value of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 7. The method of claim 1, further comprising determining the COVID-19 disease state of the subject with a negative predictive value of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 8. The method of claim 1, further comprising determining the COVID-19 disease state of the subject with an Area-Under-Curve (AUC) of at least about 0.50, at least about 0.55, at least about 0.60, at least about 0.65, at least about 0.70, at least about 0.75, at least about 0.80, at least about 0.85, at least about 0.90, at least about 0.91, at least about 0.92, at least about 0.93, at least about 0.94, at least about 0.95, at least about 0.96, at least about 0.97, at least about 0.98, at least about 0.99, or more than about 0.99.
 9. The method of claim 1, wherein the subject has received a diagnosis of the COVID-19 disease.
 10. The method of claim 1, wherein the subject is suspected of having the COVID-19 disease.
 11. The method of claim 1, wherein the subject is at elevated risk of having the COVID-19 disease or having severe complications from the COVID-19 disease.
 12. The method of claim 1, wherein the subject is asymptomatic for the COVID-19 disease.
 13. The method of any one of claims 1 to 12, further comprising administering a treatment to the subject based at least in part on the determined COVID-19 disease state.
 14. The method of claim 13, wherein the treatment is configured to treat the COVID-19 disease state of the subject.
 15. The method of claim 13, wherein the treatment is configured to reduce a severity of the COVID-19 disease state of the subject.
 16. The method of claim 13, wherein the treatment is configured to reduce a risk of having the COVID-19 disease.
 17. The method of claim 13, wherein the treatment comprises a drug.
 18. The method of claim 17, wherein the drug is selected from the group listed in Tables 8A-8B.
 19. The method of claim 1, wherein (b) comprises using a trained machine learning classifier to analyze the data set to determine the COVID-19 disease state of the subject.
 20. The method of claim 19, wherein the trained machine learning classifier is trained using gene expression data obtained by a data analysis tool selected from the group consisting of: a BIG-C™ big data analysis tool, an I-Scope™ big data analysis tool, a T-Scope™ big data analysis tool, a CellScan big data analysis tool, an MS (Molecular Signature) Scoring™ analysis tool, and a Gene Set Variation Analysis (GSVA) tool.
 21. The method of claim 19, wherein the trained machine learning classifier is selected from the group consisting of a linear regression, a logistic regression, a Ridge regression, a Lasso regression, an elastic net (EN) regression, a support vector machine (SVM), a gradient boosted machine (GBM), a k nearest neighbors (kNN), a generalized linear model (GLM), a naïve Bayes (NB) classifier, a neural network, a Random Forest (RF), a deep learning algorithm, and a combination thereof.
 22. The method of claim 1, wherein (b) comprises comparing the data set to a reference data set.
 23. The method of claim 22, wherein the reference data set comprises gene expression measurements of reference biological samples at each of the plurality of COVID-19 disease-associated genomic loci.
 24. The method of claim 23, wherein the reference biological samples comprise a first plurality of biological samples obtained or derived from subjects having the COVID-19 disease and a second plurality of biological samples obtained or derived from subjects not having the COVID-19 disease.
 25. The method of claim 1, wherein the biological sample is selected from the group consisting of: a blood sample, isolated peripheral blood mononuclear cells (PBMCs), a biopsy sample, and any derivative thereof.
 26. The method of any one of claims 1-25, further comprising determining a likelihood of the determined COVID-19 disease state.
 27. The method of any one of claims 1 to 26, further comprising monitoring the COVID-19 disease state of the subject, wherein the monitoring comprises assessing the COVID-19 disease state of the subject at a plurality of time points.
 28. The method of claim 27, wherein a difference in the assessment of the COVID-19 disease state of the subject among the plurality of time points is indicative of one or more clinical indications selected from the group consisting of: (i) a diagnosis of the COVID-19 disease state of the subject, (ii) a prognosis of the COVID-19 disease state of the subject, and (iii) an efficacy or non-efficacy of a course of treatment for treating the COVID-19 disease state of the subject.
 29. A computer system for determining a COVID-19 disease state of a subject, comprising: a database that is configured to store a dataset comprising gene expression data, wherein the gene expression data is obtained by assaying a biological sample obtained or derived from the subject to produce gene expression measurements of the biological sample at each of a plurality of COVID-19 disease-associated genomic loci, wherein the plurality of COVID-19 disease-associated genomic loci comprises at least a portion of a gene selected from the group of genes listed in Table 6 and Tables 7A-7C; and one or more computer processors operatively coupled to the database, wherein the one or more computer processors are individually or collectively programmed to: (i) computer process the data set to determine the COVID-19 disease state of the subject; (ii) electronically output a report indicative of the COVID-19 disease state of the subject.
 30. The computer system of claim 29, further comprising an electronic display operatively coupled to the one or more computer processors, wherein the electronic display comprises a graphical user interface that is configured to display the report.
 31. The computer system of claim 29, wherein the plurality of COVID-19 disease-associated genomic loci comprises at least a portion of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000, 5100, 5200, 5300, 5400, 5500, 5600, 5700, 5800, 5900, or 6000 genes selected from the group of genes listed in Table 6 and Tables 7A-7C.
 32. The computer system of claim 29, wherein the one or more computer processors are individually or collectively programmed to further determine the COVID-19 disease state of the subject with an accuracy of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 33. The computer system of claim 29, wherein the one or more computer processors are individually or collectively programmed to further determine the COVID-19 disease state of the subject with a sensitivity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 34. The computer system of claim 29, wherein the one or more computer processors are individually or collectively programmed to further determine the COVID-19 disease state of the subject with a specificity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 35. The computer system of claim 29, wherein the one or more computer processors are individually or collectively programmed to further determine the COVID-19 disease state of the subject with a positive predictive value of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 36. The computer system of claim 29, wherein the one or more computer processors are individually or collectively programmed to further determine the COVID-19 disease state of the subject with a negative predictive value of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 37. The computer system of claim 29, wherein the one or more computer processors are individually or collectively programmed to further determine the COVID-19 disease state of the subject with an Area-Under-Curve (AUC) of at least about 0.50, at least about 0.55, at least about 0.60, at least about 0.65, at least about 0.70, at least about 0.75, at least about 0.80, at least about 0.85, at least about 0.90, at least about 0.91, at least about 0.92, at least about 0.93, at least about 0.94, at least about 0.95, at least about 0.96, at least about 0.97, at least about 0.98, at least about 0.99, or more than about 0.99.
 38. The computer system of claim 29, wherein the subject has received a diagnosis of the COVID-19 disease.
 39. The computer system of claim 29, wherein the subject is suspected of having the COVID-19 disease.
 40. The computer system of claim 29, wherein the subject is at elevated risk of having the COVID-19 disease or having severe complications from the COVID-19 disease.
 41. The computer system of claim 29, wherein the subject is asymptomatic for the COVID-19 disease.
 42. The computer system of any one of claims 29-41, wherein the one or more computer processors are individually or collectively programmed to further direct a treatment to be administered to the subject based at least in part on the determined COVID-19 disease state.
 43. The computer system of claim 42, wherein the treatment is configured to treat the COVID-19 disease state of the subject.
 44. The computer system of claim 42, wherein the treatment is configured to reduce a severity of the COVID-19 disease state of the subject.
 45. The computer system of claim 42, wherein the treatment is configured to reduce a risk of having the COVID-19 disease.
 46. The computer system of claim 42, wherein the treatment comprises a drug.
 47. The computer system of claim 46, wherein the drug is selected from the group listed in Tables 8A-8B.
 48. The computer system of claim 29, wherein (i) comprises using a trained machine learning classifier to analyze the data set to determine the COVID-19 disease state of the subject.
 49. The computer system of claim 48, wherein the trained machine learning classifier is trained using gene expression data obtained by a data analysis tool selected from the group consisting of: a BIG-C™ big data analysis tool, an I-Scope™ big data analysis tool, a T-Scope™ big data analysis tool, a CellScan big data analysis tool, an MS (Molecular Signature) Scoring™ analysis tool, and a Gene Set Variation Analysis (GSVA) tool.
 50. The computer system of claim 48, wherein the trained machine learning classifier is selected from the group consisting of a linear regression, a logistic regression, a Ridge regression, a Lasso regression, an elastic net (EN) regression, a support vector machine (SVM), a gradient boosted machine (GBM), a k nearest neighbors (kNN), a generalized linear model (GLM), a naïve Bayes (NB) classifier, a neural network, a Random Forest (RF), a deep learning algorithm, and a combination thereof.
 51. The computer system of claim 29, wherein (i) comprises comparing the data set to a reference data set.
 52. The computer system of claim 51, wherein the reference data set comprises gene expression measurements of reference biological samples at each of the plurality of COVID-19 disease-associated genomic loci.
 53. The computer system of claim 52, wherein the reference biological samples comprise a first plurality of biological samples obtained or derived from subjects having the COVID-19 disease and a second plurality of biological samples obtained or derived from subjects not having the COVID-19 disease.
 54. The computer system of claim 29, wherein the biological sample is selected from the group consisting of: a blood sample, isolated peripheral blood mononuclear cells (PBMCs), a biopsy sample, and any derivative thereof.
 55. The computer system of any one of claims 29-54, wherein the one or more computer processors are individually or collectively programmed to further determine a likelihood of the determined COVID-19 disease state.
 56. The computer system of any one of claims 29-55, wherein the one or more computer processors are individually or collectively programmed to further monitor the COVID-19 disease state of the subject, wherein the monitoring comprises assessing the COVID-19 disease state of the subject at a plurality of time points.
 57. The computer system of claim 56, wherein a difference in the assessment of the COVID-19 disease state of the subject among the plurality of time points is indicative of one or more clinical indications selected from the group consisting of: (i) a diagnosis of the COVID-19 disease state of the subject, (ii) a prognosis of the COVID-19 disease state of the subject, and (iii) an efficacy or non-efficacy of a course of treatment for treating the COVID-19 disease state of the subject.
 58. A non-transitory computer readable medium comprising machine-executable code that, upon execution by one or more computer processors, implements a method for determining a COVID-19 disease state of a subject, the method comprising: (a) assaying a biological sample obtained or derived from the subject to produce a data set comprising gene expression measurements of the biological sample at each of a plurality of COVID-19 disease-associated genomic loci, wherein the plurality of COVID-19 disease-associated genomic loci comprises at least a portion of a gene selected from the group of genes listed in Table 6 and Tables 7A-7C; (b) computer processing the data set to determine the COVID-19 disease state of the subject; and (c) electronically outputting a report indicative of the COVID-19 disease state of the subject.
 59. The non-transitory computer readable medium of claim 58, wherein the plurality of COVID-19 disease-associated genomic loci comprises at least a portion of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000, 5100, 5200, 5300, 5400, 5500, 5600, 5700, 5800, 5900, or 6000 genes selected from the group of genes listed in Table 6 and Tables 7A-7C.
 60. The non-transitory computer readable medium of claim 58, further comprising determining the COVID-19 disease state of the subject with an accuracy of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 61. The non-transitory computer readable medium of claim 58, further comprising determining the COVID-19 disease state of the subject with a sensitivity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 62. The non-transitory computer readable medium of claim 58, further comprising determining the COVID-19 disease state of the subject with a specificity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 63. The non-transitory computer readable medium of claim 58, further comprising determining the COVID-19 disease state of the subject with a positive predictive value of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 64. The non-transitory computer readable medium of claim 58, further comprising determining the COVID-19 disease state of the subject with a negative predictive value of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than about 99%.
 65. The non-transitory computer readable medium of claim 58, further comprising determining the COVID-19 disease state of the subject with an Area-Under-Curve (AUC) of at least about 0.50, at least about 0.55, at least about 0.60, at least about 0.65, at least about 0.70, at least about 0.75, at least about 0.80, at least about 0.85, at least about 0.90, at least about 0.91, at least about 0.92, at least about 0.93, at least about 0.94, at least about 0.95, at least about 0.96, at least about 0.97, at least about 0.98, at least about 0.99, or more than about 0.99.
 66. The non-transitory computer readable medium of claim 58, wherein the subject has received a diagnosis of the COVID-19 disease.
 67. The non-transitory computer readable medium of claim 58, wherein the subject is suspected of having the COVID-19 disease.
 68. The non-transitory computer readable medium of claim 58, wherein the subject is at elevated risk of having the COVID-19 disease or having severe complications from the COVID-19 disease.
 69. The non-transitory computer readable medium of claim 58, wherein the subject is asymptomatic for the COVID-19 disease.
 70. The non-transitory computer readable medium of any one of claims 58-69, further comprising directing a treatment to be administered to the subject based at least in part on the determined COVID-19 disease state.
 71. The non-transitory computer readable medium of claim 70, wherein the treatment is configured to treat the COVID-19 disease state of the subject.
 72. The non-transitory computer readable medium of claim 70, wherein the treatment is configured to reduce a severity of the COVID-19 disease state of the subject.
 73. The non-transitory computer readable medium of claim 70, wherein the treatment is configured to reduce a risk of having the COVID-19 disease.
 74. The non-transitory computer readable medium of claim 70, wherein the treatment comprises a drug.
 75. The non-transitory computer readable medium of claim 74, wherein the drug is selected from the group listed in Tables 8A-8B.
 76. The non-transitory computer readable medium of claim 58, wherein (b) comprises using a trained machine learning classifier to analyze the data set to determine the COVID-19 disease state of the subject.
 77. The non-transitory computer readable medium of claim 76, wherein the trained machine learning classifier is trained using gene expression data obtained by a data analysis tool selected from the group consisting of: a BIG-C™ big data analysis tool, an I-Scope™ big data analysis tool, a T-Scope™ big data analysis tool, a CellScan big data analysis tool, an MS (Molecular Signature) Scoring™ analysis tool, and a Gene Set Variation Analysis (GSVA) tool.
 78. The non-transitory computer readable medium of claim 76, wherein the trained machine learning classifier is selected from the group consisting of a linear regression, a logistic regression, a Ridge regression, a Lasso regression, an elastic net (EN) regression, a support vector machine (SVM), a gradient boosted machine (GBM), a k nearest neighbors (kNN), a generalized linear model (GLM), a naïve Bayes (NB) classifier, a neural network, a Random Forest (RF), a deep learning algorithm, and a combination thereof.
 79. The non-transitory computer readable medium of claim 58, wherein (b) comprises comparing the data set to a reference data set.
 80. The non-transitory computer readable medium of claim 79, wherein the reference data set comprises gene expression measurements of reference biological samples at each of the plurality of COVID-19 disease-associated genomic loci.
 81. The non-transitory computer readable medium of claim 80, wherein the reference biological samples comprise a first plurality of biological samples obtained or derived from subjects having the COVID-19 disease and a second plurality of biological samples obtained or derived from subjects not having the COVID-19 disease.
 82. The non-transitory computer readable medium of claim 58, wherein the biological sample is selected from the group consisting of: a blood sample, isolated peripheral blood mononuclear cells (PBMCs), a biopsy sample, and any derivative thereof.
 83. The non-transitory computer readable medium of any one of claims 58-82, further comprising determining a likelihood of the determined COVID-19 disease state.
 84. The non-transitory computer readable medium of any one of claims 58-83, further comprising monitoring the COVID-19 disease state of the subject, wherein the monitoring comprises assessing the COVID-19 disease state of the subject at a plurality of time points.
 85. The non-transitory computer readable medium of claim 84, wherein a difference in the assessment of the COVID-19 disease state of the subject among the plurality of time points is indicative of one or more clinical indications selected from the group consisting of: (i) a diagnosis of the COVID-19 disease state of the subject, (ii) a prognosis of the COVID-19 disease state of the subject, and (iii) an efficacy or non-efficacy of a course of treatment for treating the COVID-19 disease state of the subject. 